PDB Short entry for 2QBX HEADER SIGNALING PROTEIN 18-JUN-07 2QBX TITLE EPHB2/SNEW ANTAGONISTIC PEPTIDE COMPLEX CAVEAT 2QBX CHIRALITY ERROR AT CA IN ALA39 CHAIN B COMPND MOL_ID: 1; COMPND 2 MOLECULE: EPHRIN TYPE-B RECEPTOR 2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: EPHB2; COMPND 5 SYNONYM: TYROSINE-PROTEIN KINASE RECEPTOR EPH-3; COMPND 6 EC: 2.7.10.1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: ANTAGONISTIC PEPTIDE; COMPND 10 CHAIN: D, P; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: EPHB2, DRT, EPHT3, EPTH3, ERK, HEK5, TYRO5; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: HI-5; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PFASTBAC1; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PBAC6; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 OTHER_DETAILS: ANTAGONISTIC PEPTIDE KEYWDS RECEPTOR TYROSINE KINASE, BI-DIRECTIONAL SIGNALING, TUMORIGENESIS, KEYWDS 2 ANGIOGENESIS, SIGNALING PROTEIN, STRUCTURAL GENOMICS, PSI-2, PROTEIN KEYWDS 3 STRUCTURE INITIATIVE, ACCELERATED TECHNOLOGIES CENTER FOR GENE TO 3D KEYWDS 4 STRUCTURE, ATCG3D EXPDTA X-RAY DIFFRACTION AUTHOR J.E.CHRENCIK,A.BROOUN,M.I.RECHT,G.NICOLA,E.B.PASQUALE,P.KUHN, AUTHOR 2 ACCELERATED TECHNOLOGIES CENTER FOR GENE TO 3D STRUCTURE (ATCG3D) REVDAT 4 30-AUG-23 2QBX 1 REMARK SEQADV REVDAT 3 08-SEP-09 2QBX 1 AUTHOR JRNL REVDAT 2 24-FEB-09 2QBX 1 VERSN REVDAT 1 06-NOV-07 2QBX 0 JRNL AUTH J.E.CHRENCIK,A.BROOUN,M.I.RECHT,G.NICOLA,L.K.DAVIS, JRNL AUTH 2 R.ABAGYAN,H.WIDMER,E.B.PASQUALE,P.KUHN JRNL TITL THREE-DIMENSIONAL STRUCTURE OF THE EPHB2 RECEPTOR IN COMPLEX JRNL TITL 2 WITH AN ANTAGONISTIC PEPTIDE REVEALS A NOVEL MODE OF JRNL TITL 3 INHIBITION. JRNL REF J.BIOL.CHEM. V. 282 36505 2007 JRNL REFN ISSN 0021-9258 JRNL PMID 17897949 JRNL DOI 10.1074/JBC.M706340200 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 17391 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 942 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1174 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.06 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE SET COUNT : 71 REMARK 3 BIN FREE R VALUE : 0.3130 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2979 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 174 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.23000 REMARK 3 B22 (A**2) : 0.23000 REMARK 3 B33 (A**2) : -0.35000 REMARK 3 B12 (A**2) : 0.12000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.395 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.275 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.206 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.396 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.896 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3130 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2651 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4261 ; 2.106 ; 1.942 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6150 ; 1.295 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 373 ;19.432 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 150 ;35.724 ;23.467 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 488 ;16.254 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;16.122 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 439 ; 0.217 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3442 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 683 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 523 ; 0.199 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2765 ; 0.207 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1455 ; 0.195 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1828 ; 0.097 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 176 ; 0.200 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.068 ; 0.200 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 14 ; 0.100 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 69 ; 0.263 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.338 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2003 ; 0.939 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 760 ; 0.178 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3012 ; 1.416 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1437 ; 1.834 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1246 ; 2.663 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2QBX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000043405. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17391 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.299 REMARK 200 RESOLUTION RANGE LOW (A) : 34.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1NUK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES, PH 7.2, 100 MM AMMONIUM REMARK 280 SULFATE, AND 20% PEG-3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 156.68333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 78.34167 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE BIOLOGICAL UNIT IS A DIMER. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5510 ANGSTROM**2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D, P REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -3 REMARK 465 VAL A -2 REMARK 465 SER A -1 REMARK 465 ALA A 0 REMARK 465 ILE A 1 REMARK 465 VAL A 2 REMARK 465 LEU A 3 REMARK 465 TYR A 4 REMARK 465 VAL A 5 REMARK 465 LEU A 6 REMARK 465 LEU A 7 REMARK 465 ALA A 8 REMARK 465 ALA A 9 REMARK 465 ALA A 10 REMARK 465 ALA A 11 REMARK 465 HIS A 12 REMARK 465 SER A 13 REMARK 465 ALA A 14 REMARK 465 PHE A 15 REMARK 465 ALA A 16 REMARK 465 ALA A 17 REMARK 465 MET A 18 REMARK 465 VAL A 19 REMARK 465 HIS A 20 REMARK 465 HIS A 21 REMARK 465 HIS A 22 REMARK 465 HIS A 23 REMARK 465 HIS A 24 REMARK 465 HIS A 25 REMARK 465 SER A 26 REMARK 465 ALA A 27 REMARK 465 LYS A 204 REMARK 465 MET B -3 REMARK 465 VAL B -2 REMARK 465 SER B -1 REMARK 465 ALA B 0 REMARK 465 ILE B 1 REMARK 465 VAL B 2 REMARK 465 LEU B 3 REMARK 465 TYR B 4 REMARK 465 VAL B 5 REMARK 465 LEU B 6 REMARK 465 LEU B 7 REMARK 465 ALA B 8 REMARK 465 ALA B 9 REMARK 465 ALA B 10 REMARK 465 ALA B 11 REMARK 465 HIS B 12 REMARK 465 SER B 13 REMARK 465 ALA B 14 REMARK 465 PHE B 15 REMARK 465 ALA B 16 REMARK 465 ALA B 17 REMARK 465 MET B 18 REMARK 465 VAL B 19 REMARK 465 HIS B 20 REMARK 465 HIS B 21 REMARK 465 HIS B 22 REMARK 465 HIS B 23 REMARK 465 HIS B 24 REMARK 465 HIS B 25 REMARK 465 SER B 26 REMARK 465 ALA B 27 REMARK 465 LYS B 204 REMARK 465 HIS D 12 REMARK 465 PRO P 10 REMARK 465 GLN P 11 REMARK 465 HIS P 12 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 40 CD OE1 OE2 REMARK 470 ARG A 87 NE CZ NH1 NH2 REMARK 470 ARG A 89 NE CZ NH1 NH2 REMARK 470 LYS A 133 CG CD CE NZ REMARK 470 SER A 156 OG REMARK 470 GLU B 40 CD OE1 OE2 REMARK 470 GLU B 52 CD OE1 OE2 REMARK 470 GLU B 74 CD OE1 OE2 REMARK 470 ARG B 87 NE CZ NH1 NH2 REMARK 470 ARG B 89 CD NE CZ NH1 NH2 REMARK 470 LYS B 133 CG CD CE NZ REMARK 470 SER B 156 OG REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 SER B 49 N - CA - CB ANGL. DEV. = -9.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU A 40 141.55 -35.89 REMARK 500 CYS A 70 59.80 -158.53 REMARK 500 ASN A 71 54.97 -95.48 REMARK 500 ASP A 104 70.73 37.43 REMARK 500 ASN A 141 75.66 68.08 REMARK 500 ALA B 39 -156.16 -154.20 REMARK 500 ASP B 58 -158.44 -97.27 REMARK 500 CYS B 70 65.63 -156.16 REMARK 500 ASN B 71 52.79 -98.42 REMARK 500 ARG B 89 47.60 38.00 REMARK 500 ASN B 141 76.63 69.07 REMARK 500 ASP B 152 -161.66 -109.28 REMARK 500 TYR B 202 -155.51 -139.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TYR A 57 ASP A 58 146.03 REMARK 500 ARG A 103 ASP A 104 113.62 REMARK 500 ASN A 141 PRO A 142 50.99 REMARK 500 LEU A 160 GLY A 161 -125.65 REMARK 500 ALA B 39 GLU B 40 143.04 REMARK 500 ASP B 58 GLU B 59 -137.16 REMARK 500 THR B 63 ILE B 64 -141.89 REMARK 500 ASN B 141 PRO B 142 48.39 REMARK 500 VAL B 164 MET B 165 132.99 REMARK 500 TYR B 202 ARG B 203 -118.46 REMARK 500 PRO D 10 GLN D 11 -138.11 REMARK 500 ARG P 8 LEU P 9 95.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 412 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NUK RELATED DB: PDB REMARK 900 APO LIGAND BINDING DOMAIN OF THE EPHB2 RECEPTOR REMARK 900 RELATED ID: 1KGY RELATED DB: PDB REMARK 900 EPHB2/EPHRINB2 COMPLEX STRUCTURE REMARK 900 RELATED ID: 2BBA RELATED DB: PDB REMARK 900 EPHB4/ANTAGONISTIC TNYL-RAW COMPLEX STRUCTURE DBREF 2QBX A 28 204 UNP P29323 EPHB2_HUMAN 20 196 DBREF 2QBX B 28 204 UNP P29323 EPHB2_HUMAN 20 196 DBREF 2QBX D 1 12 PDB 2QBX 2QBX 1 12 DBREF 2QBX P 1 12 PDB 2QBX 2QBX 1 12 SEQADV 2QBX MET A -3 UNP P29323 EXPRESSION TAG SEQADV 2QBX VAL A -2 UNP P29323 EXPRESSION TAG SEQADV 2QBX SER A -1 UNP P29323 EXPRESSION TAG SEQADV 2QBX ALA A 0 UNP P29323 EXPRESSION TAG SEQADV 2QBX ILE A 1 UNP P29323 EXPRESSION TAG SEQADV 2QBX VAL A 2 UNP P29323 EXPRESSION TAG SEQADV 2QBX LEU A 3 UNP P29323 EXPRESSION TAG SEQADV 2QBX TYR A 4 UNP P29323 EXPRESSION TAG SEQADV 2QBX VAL A 5 UNP P29323 EXPRESSION TAG SEQADV 2QBX LEU A 6 UNP P29323 EXPRESSION TAG SEQADV 2QBX LEU A 7 UNP P29323 EXPRESSION TAG SEQADV 2QBX ALA A 8 UNP P29323 EXPRESSION TAG SEQADV 2QBX ALA A 9 UNP P29323 EXPRESSION TAG SEQADV 2QBX ALA A 10 UNP P29323 EXPRESSION TAG SEQADV 2QBX ALA A 11 UNP P29323 EXPRESSION TAG SEQADV 2QBX HIS A 12 UNP P29323 EXPRESSION TAG SEQADV 2QBX SER A 13 UNP P29323 EXPRESSION TAG SEQADV 2QBX ALA A 14 UNP P29323 EXPRESSION TAG SEQADV 2QBX PHE A 15 UNP P29323 EXPRESSION TAG SEQADV 2QBX ALA A 16 UNP P29323 EXPRESSION TAG SEQADV 2QBX ALA A 17 UNP P29323 EXPRESSION TAG SEQADV 2QBX MET A 18 UNP P29323 EXPRESSION TAG SEQADV 2QBX VAL A 19 UNP P29323 EXPRESSION TAG SEQADV 2QBX HIS A 20 UNP P29323 EXPRESSION TAG SEQADV 2QBX HIS A 21 UNP P29323 EXPRESSION TAG SEQADV 2QBX HIS A 22 UNP P29323 EXPRESSION TAG SEQADV 2QBX HIS A 23 UNP P29323 EXPRESSION TAG SEQADV 2QBX HIS A 24 UNP P29323 EXPRESSION TAG SEQADV 2QBX HIS A 25 UNP P29323 EXPRESSION TAG SEQADV 2QBX SER A 26 UNP P29323 EXPRESSION TAG SEQADV 2QBX ALA A 27 UNP P29323 EXPRESSION TAG SEQADV 2QBX MET B -3 UNP P29323 EXPRESSION TAG SEQADV 2QBX VAL B -2 UNP P29323 EXPRESSION TAG SEQADV 2QBX SER B -1 UNP P29323 EXPRESSION TAG SEQADV 2QBX ALA B 0 UNP P29323 EXPRESSION TAG SEQADV 2QBX ILE B 1 UNP P29323 EXPRESSION TAG SEQADV 2QBX VAL B 2 UNP P29323 EXPRESSION TAG SEQADV 2QBX LEU B 3 UNP P29323 EXPRESSION TAG SEQADV 2QBX TYR B 4 UNP P29323 EXPRESSION TAG SEQADV 2QBX VAL B 5 UNP P29323 EXPRESSION TAG SEQADV 2QBX LEU B 6 UNP P29323 EXPRESSION TAG SEQADV 2QBX LEU B 7 UNP P29323 EXPRESSION TAG SEQADV 2QBX ALA B 8 UNP P29323 EXPRESSION TAG SEQADV 2QBX ALA B 9 UNP P29323 EXPRESSION TAG SEQADV 2QBX ALA B 10 UNP P29323 EXPRESSION TAG SEQADV 2QBX ALA B 11 UNP P29323 EXPRESSION TAG SEQADV 2QBX HIS B 12 UNP P29323 EXPRESSION TAG SEQADV 2QBX SER B 13 UNP P29323 EXPRESSION TAG SEQADV 2QBX ALA B 14 UNP P29323 EXPRESSION TAG SEQADV 2QBX PHE B 15 UNP P29323 EXPRESSION TAG SEQADV 2QBX ALA B 16 UNP P29323 EXPRESSION TAG SEQADV 2QBX ALA B 17 UNP P29323 EXPRESSION TAG SEQADV 2QBX MET B 18 UNP P29323 EXPRESSION TAG SEQADV 2QBX VAL B 19 UNP P29323 EXPRESSION TAG SEQADV 2QBX HIS B 20 UNP P29323 EXPRESSION TAG SEQADV 2QBX HIS B 21 UNP P29323 EXPRESSION TAG SEQADV 2QBX HIS B 22 UNP P29323 EXPRESSION TAG SEQADV 2QBX HIS B 23 UNP P29323 EXPRESSION TAG SEQADV 2QBX HIS B 24 UNP P29323 EXPRESSION TAG SEQADV 2QBX HIS B 25 UNP P29323 EXPRESSION TAG SEQADV 2QBX SER B 26 UNP P29323 EXPRESSION TAG SEQADV 2QBX ALA B 27 UNP P29323 EXPRESSION TAG SEQRES 1 A 208 MET VAL SER ALA ILE VAL LEU TYR VAL LEU LEU ALA ALA SEQRES 2 A 208 ALA ALA HIS SER ALA PHE ALA ALA MET VAL HIS HIS HIS SEQRES 3 A 208 HIS HIS HIS SER ALA GLU GLU THR LEU MET ASP SER THR SEQRES 4 A 208 THR ALA THR ALA GLU LEU GLY TRP MET VAL HIS PRO PRO SEQRES 5 A 208 SER GLY TRP GLU GLU VAL SER GLY TYR ASP GLU ASN MET SEQRES 6 A 208 ASN THR ILE ARG THR TYR GLN VAL CYS ASN VAL PHE GLU SEQRES 7 A 208 SER SER GLN ASN ASN TRP LEU ARG THR LYS PHE ILE ARG SEQRES 8 A 208 ARG ARG GLY ALA HIS ARG ILE HIS VAL GLU MET LYS PHE SEQRES 9 A 208 SER VAL ARG ASP CYS SER SER ILE PRO SER VAL PRO GLY SEQRES 10 A 208 SER CYS LYS GLU THR PHE ASN LEU TYR TYR TYR GLU ALA SEQRES 11 A 208 ASP PHE ASP SER ALA THR LYS THR PHE PRO ASN TRP MET SEQRES 12 A 208 GLU ASN PRO TRP VAL LYS VAL ASP THR ILE ALA ALA ASP SEQRES 13 A 208 GLU SER PHE SER GLN VAL ASP LEU GLY GLY ARG VAL MET SEQRES 14 A 208 LYS ILE ASN THR GLU VAL ARG SER PHE GLY PRO VAL SER SEQRES 15 A 208 ARG SER GLY PHE TYR LEU ALA PHE GLN ASP TYR GLY GLY SEQRES 16 A 208 CYS MET SER LEU ILE ALA VAL ARG VAL PHE TYR ARG LYS SEQRES 1 B 208 MET VAL SER ALA ILE VAL LEU TYR VAL LEU LEU ALA ALA SEQRES 2 B 208 ALA ALA HIS SER ALA PHE ALA ALA MET VAL HIS HIS HIS SEQRES 3 B 208 HIS HIS HIS SER ALA GLU GLU THR LEU MET ASP SER THR SEQRES 4 B 208 THR ALA THR ALA GLU LEU GLY TRP MET VAL HIS PRO PRO SEQRES 5 B 208 SER GLY TRP GLU GLU VAL SER GLY TYR ASP GLU ASN MET SEQRES 6 B 208 ASN THR ILE ARG THR TYR GLN VAL CYS ASN VAL PHE GLU SEQRES 7 B 208 SER SER GLN ASN ASN TRP LEU ARG THR LYS PHE ILE ARG SEQRES 8 B 208 ARG ARG GLY ALA HIS ARG ILE HIS VAL GLU MET LYS PHE SEQRES 9 B 208 SER VAL ARG ASP CYS SER SER ILE PRO SER VAL PRO GLY SEQRES 10 B 208 SER CYS LYS GLU THR PHE ASN LEU TYR TYR TYR GLU ALA SEQRES 11 B 208 ASP PHE ASP SER ALA THR LYS THR PHE PRO ASN TRP MET SEQRES 12 B 208 GLU ASN PRO TRP VAL LYS VAL ASP THR ILE ALA ALA ASP SEQRES 13 B 208 GLU SER PHE SER GLN VAL ASP LEU GLY GLY ARG VAL MET SEQRES 14 B 208 LYS ILE ASN THR GLU VAL ARG SER PHE GLY PRO VAL SER SEQRES 15 B 208 ARG SER GLY PHE TYR LEU ALA PHE GLN ASP TYR GLY GLY SEQRES 16 B 208 CYS MET SER LEU ILE ALA VAL ARG VAL PHE TYR ARG LYS SEQRES 1 D 12 SER ASN GLU TRP ILE GLN PRO ARG LEU PRO GLN HIS SEQRES 1 P 12 SER ASN GLU TRP ILE GLN PRO ARG LEU PRO GLN HIS HET SO4 A 404 5 HET SO4 A 405 5 HET SO4 A 406 5 HET SO4 A 408 5 HET SO4 B 401 5 HET SO4 B 402 5 HET SO4 B 403 5 HET SO4 B 409 5 HET SO4 B 410 5 HET SO4 B 411 5 HET SO4 B 412 5 HET SO4 D 407 5 HETNAM SO4 SULFATE ION FORMUL 5 SO4 12(O4 S 2-) FORMUL 17 HOH *174(H2 O) HELIX 1 1 THR A 35 ALA A 37 5 3 HELIX 2 2 ASP A 104 ILE A 108 5 5 HELIX 3 3 THR B 35 ALA B 37 5 3 HELIX 4 4 ASP B 104 ILE B 108 5 5 SHEET 1 A 4 GLU A 29 ASP A 33 0 SHEET 2 A 4 MET A 193 TYR A 202 -1 O VAL A 200 N MET A 32 SHEET 3 A 4 THR A 63 VAL A 69 -1 N TYR A 67 O LEU A 195 SHEET 4 A 4 GLU A 52 TYR A 57 -1 N GLY A 56 O ILE A 64 SHEET 1 B 5 GLU A 29 ASP A 33 0 SHEET 2 B 5 MET A 193 TYR A 202 -1 O VAL A 200 N MET A 32 SHEET 3 B 5 ILE A 94 VAL A 102 -1 N HIS A 95 O PHE A 201 SHEET 4 B 5 ARG A 163 PHE A 174 -1 O ARG A 172 N VAL A 96 SHEET 5 B 5 SER A 156 LEU A 160 -1 N LEU A 160 O ARG A 163 SHEET 1 C 4 MET A 44 HIS A 46 0 SHEET 2 C 4 ASN A 79 ARG A 82 -1 O TRP A 80 N HIS A 46 SHEET 3 C 4 GLY A 181 ASP A 188 -1 O ASP A 188 N ASN A 79 SHEET 4 C 4 ILE A 86 ARG A 87 -1 N ILE A 86 O PHE A 182 SHEET 1 D 5 MET A 44 HIS A 46 0 SHEET 2 D 5 ASN A 79 ARG A 82 -1 O TRP A 80 N HIS A 46 SHEET 3 D 5 GLY A 181 ASP A 188 -1 O ASP A 188 N ASN A 79 SHEET 4 D 5 PHE A 119 ALA A 126 -1 N TYR A 124 O TYR A 183 SHEET 5 D 5 VAL A 144 ILE A 149 -1 O ILE A 149 N PHE A 119 SHEET 1 E 4 GLU B 29 ASP B 33 0 SHEET 2 E 4 CYS B 192 TYR B 202 -1 O VAL B 200 N LEU B 31 SHEET 3 E 4 THR B 63 CYS B 70 -1 N TYR B 67 O LEU B 195 SHEET 4 E 4 GLU B 52 TYR B 57 -1 N VAL B 54 O THR B 66 SHEET 1 F 5 GLU B 29 ASP B 33 0 SHEET 2 F 5 CYS B 192 TYR B 202 -1 O VAL B 200 N LEU B 31 SHEET 3 F 5 ILE B 94 VAL B 102 -1 N HIS B 95 O PHE B 201 SHEET 4 F 5 VAL B 164 PHE B 174 -1 O ARG B 172 N VAL B 96 SHEET 5 F 5 SER B 156 ASP B 159 -1 N VAL B 158 O MET B 165 SHEET 1 G 4 MET B 44 HIS B 46 0 SHEET 2 G 4 ASN B 79 ARG B 82 -1 O TRP B 80 N HIS B 46 SHEET 3 G 4 GLY B 181 ASP B 188 -1 O ASP B 188 N ASN B 79 SHEET 4 G 4 ILE B 86 ARG B 87 -1 N ILE B 86 O PHE B 182 SHEET 1 H 5 MET B 44 HIS B 46 0 SHEET 2 H 5 ASN B 79 ARG B 82 -1 O TRP B 80 N HIS B 46 SHEET 3 H 5 GLY B 181 ASP B 188 -1 O ASP B 188 N ASN B 79 SHEET 4 H 5 THR B 118 ALA B 126 -1 N ALA B 126 O GLY B 181 SHEET 5 H 5 VAL B 144 ALA B 150 -1 O ILE B 149 N PHE B 119 SSBOND 1 CYS A 70 CYS A 192 1555 1555 2.07 SSBOND 2 CYS A 105 CYS A 115 1555 1555 1.68 SSBOND 3 CYS B 70 CYS B 192 1555 1555 2.05 SSBOND 4 CYS B 105 CYS B 115 1555 1555 2.06 CISPEP 1 HIS A 46 PRO A 47 0 2.27 CISPEP 2 PHE A 135 PRO A 136 0 -7.66 CISPEP 3 GLY A 161 GLY A 162 0 -3.11 CISPEP 4 GLY A 175 PRO A 176 0 -2.17 CISPEP 5 HIS B 46 PRO B 47 0 -2.27 CISPEP 6 PHE B 135 PRO B 136 0 -8.23 CISPEP 7 GLY B 175 PRO B 176 0 2.07 SITE 1 AC1 2 HIS B 95 ARG B 203 SITE 1 AC2 3 ARG B 88 GLY B 90 HIS B 92 SITE 1 AC3 4 MET B 32 ASP B 33 LEU B 41 HOH B 470 SITE 1 AC4 5 PHE A 135 PRO A 136 ASN A 137 PRO A 142 SITE 2 AC4 5 HOH A 481 SITE 1 AC5 3 ARG A 179 HOH A 480 ARG B 179 SITE 1 AC6 2 SER A 55 ARG A 65 SITE 1 AC7 5 PRO A 109 SER A 110 HOH B 441 GLN D 6 SITE 2 AC7 5 HOH D 285 SITE 1 AC8 3 ARG A 88 GLY A 90 HIS A 92 SITE 1 AC9 4 THR B 36 SER B 75 SER B 76 SER B 114 SITE 1 BC1 4 PRO B 109 SER B 110 GLN P 6 HOH P 14 SITE 1 BC2 7 TRP B 80 TYR B 122 MET B 139 GLU B 140 SITE 2 BC2 7 GLN B 187 HOH B 453 HOH B 491 SITE 1 BC3 2 SER B 55 ARG B 65 CRYST1 40.183 40.183 235.025 90.00 90.00 120.00 P 32 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.024886 0.014368 0.000000 0.00000 SCALE2 0.000000 0.028736 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004255 0.00000