PDB Short entry for 2BBA HEADER SIGNALING PROTEIN 17-OCT-05 2BBA TITLE CRYSTAL STRUCTURE AND THERMODYNAMIC CHARACTERIZATION OF THE EPHB4 TITLE 2 RECEPTOR IN COMPLEX WITH AN EPHRIN-B2 ANTAGONIST PEPTIDE REVEALS THE TITLE 3 DETERMINANTS FOR RECEPTOR SPECIFICITY. COMPND MOL_ID: 1; COMPND 2 MOLECULE: EPHRIN TYPE-B RECEPTOR 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIGAND BINDING DOMAIN; COMPND 5 SYNONYM: TYROSINE-PROTEIN KINASE RECEPTOR HTK; COMPND 6 EC: 2.7.1.112; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: AGONIST PEPTIDE; COMPND 10 CHAIN: 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: EPHB4, HTK; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: HII-5; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PBAC6; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 OTHER_DETAILS: SYNTHETIC PEPTIDE KEYWDS EPHB4, TUMORIGENESIS, ANGIOGENESIS, PEPTIDE MIMETICS, SIGNALING KEYWDS 2 PROTEIN, STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, KEYWDS 3 ACCELERATED TECHNOLOGIES CENTER FOR GENE TO 3D STRUCTURE, ATCG3D EXPDTA X-RAY DIFFRACTION AUTHOR J.E.CHRENCIK,P.KUHN,ACCELERATED TECHNOLOGIES CENTER FOR GENE TO 3D AUTHOR 2 STRUCTURE (ATCG3D) REVDAT 5 23-AUG-23 2BBA 1 REMARK SEQADV REVDAT 4 13-JUL-11 2BBA 1 VERSN REVDAT 3 01-SEP-09 2BBA 1 TITLE KEYWDS AUTHOR REVDAT 2 24-FEB-09 2BBA 1 VERSN REVDAT 1 18-JUL-06 2BBA 0 JRNL AUTH J.E.CHRENCIK,A.BROOUN,M.I.RECHT,M.L.KRAUS,M.KOOLPE, JRNL AUTH 2 A.R.KOLATKAR,R.H.BRUCE,G.MARTINY-BARON,H.WIDMER, JRNL AUTH 3 E.B.PASQUALE,P.KUHN JRNL TITL STRUCTURE AND THERMODYNAMIC CHARACTERIZATION OF THE JRNL TITL 2 EPHB4/EPHRIN-B2 ANTAGONIST PEPTIDE COMPLEX REVEALS THE JRNL TITL 3 DETERMINANTS FOR RECEPTOR SPECIFICITY. JRNL REF STRUCTURE V. 14 321 2006 JRNL REFN ISSN 0969-2126 JRNL PMID 16472751 JRNL DOI 10.1016/J.STR.2005.11.011 REMARK 2 REMARK 2 RESOLUTION. 1.65 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 31786 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) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3533 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2286 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.94 REMARK 3 BIN R VALUE (WORKING SET) : 0.1590 REMARK 3 BIN FREE R VALUE SET COUNT : 243 REMARK 3 BIN FREE R VALUE : 0.2020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1558 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 223 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.21000 REMARK 3 B22 (A**2) : 0.21000 REMARK 3 B33 (A**2) : -0.42000 REMARK 3 B12 (A**2) : 0.00000 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): 0.081 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.078 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.042 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.352 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1628 ; 0.018 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1422 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2229 ; 1.731 ; 1.938 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3288 ; 0.888 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 201 ; 7.475 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 71 ;32.303 ;22.958 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 240 ;10.131 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;16.174 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 245 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1819 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 348 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 240 ; 0.272 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1331 ; 0.202 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 741 ; 0.182 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 893 ; 0.087 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 146 ; 0.162 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.001 ; 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): 12 ; 0.342 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 62 ; 0.294 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.513 ; 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): 1076 ; 1.276 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 407 ; 0.350 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1606 ; 1.730 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 710 ; 2.790 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 622 ; 3.968 ; 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 12 A 196 REMARK 3 ORIGIN FOR THE GROUP (A): 24.6075 11.8278 51.1996 REMARK 3 T TENSOR REMARK 3 T11: -0.0478 T22: -0.0117 REMARK 3 T33: -0.0318 T12: -0.0009 REMARK 3 T13: 0.0027 T23: -0.0023 REMARK 3 L TENSOR REMARK 3 L11: 1.2085 L22: 0.2622 REMARK 3 L33: 0.4731 L12: -0.1014 REMARK 3 L13: -0.3499 L23: 0.0787 REMARK 3 S TENSOR REMARK 3 S11: 0.0000 S12: 0.0222 S13: -0.0298 REMARK 3 S21: -0.0073 S22: 0.0028 S23: -0.0081 REMARK 3 S31: -0.0146 S32: -0.0283 S33: -0.0028 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : P 251 P 264 REMARK 3 ORIGIN FOR THE GROUP (A): 31.4128 0.9273 39.8155 REMARK 3 T TENSOR REMARK 3 T11: -0.0382 T22: -0.0203 REMARK 3 T33: -0.0254 T12: 0.0060 REMARK 3 T13: 0.0478 T23: -0.0490 REMARK 3 L TENSOR REMARK 3 L11: 3.8875 L22: 1.6018 REMARK 3 L33: 6.1088 L12: 0.9516 REMARK 3 L13: 2.7544 L23: -0.3425 REMARK 3 S TENSOR REMARK 3 S11: -0.1978 S12: 0.1246 S13: -0.2250 REMARK 3 S21: -0.1392 S22: 0.1081 S23: -0.1418 REMARK 3 S31: 0.2043 S32: 0.1535 S33: 0.0897 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 2BBA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-OCT-05. REMARK 100 THE DEPOSITION ID IS D_1000034902. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAY-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 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 : SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32786 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 42.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.20800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.200 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: PDB ENTRY 1NUK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.2 M AMMONIUM SULFATE, 200 MM NACL, REMARK 280 PH 7.8, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 75.84050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.48600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.48600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.92025 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.48600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.48600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 113.76075 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.48600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.48600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.92025 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.48600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.48600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 113.76075 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 75.84050 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL 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 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 THR P 250 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 LYS A 31 CG CD CE NZ REMARK 470 GLN A 52 CG CD OE1 NE2 REMARK 470 GLN A 64 CG CD OE1 NE2 REMARK 470 ARG A 65 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 102 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 105 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 144 CG CD OE1 OE2 REMARK 470 GLU A 154 CG CD OE1 OE2 REMARK 470 LYS A 195 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 ND1 HIS A 12 C LYS A 196 1.64 REMARK 500 CD2 HIS A 12 ND1 HIS A 15 1.94 REMARK 500 ND1 HIS A 12 O LYS A 196 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS A 12 CG HIS A 12 CD2 -0.106 REMARK 500 REMARK 500 REMARK: NULL 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 HIS A 12 CB - CG - ND1 ANGL. DEV. = -8.8 DEGREES REMARK 500 ARG A 148 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 150 NE - CZ - NH1 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 150 NE - CZ - NH2 ANGL. DEV. = 4.1 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 ALA A 28 -139.21 -118.36 REMARK 500 CYS A 61 59.71 -155.45 REMARK 500 ARG A 81 -135.74 57.29 REMARK 500 ARG A 102 16.28 52.93 REMARK 500 ASN A 133 86.70 64.84 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 HIS A 12 HIS A 13 147.04 REMARK 500 ARG A 102 ALA A 103 144.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 HIS A 12 0.09 SIDE CHAIN 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 A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: ATCG3D_13 RELATED DB: TARGETDB DBREF 2BBA A 17 196 UNP P54760 EPHB4_HUMAN 17 196 DBREF 2BBA P 250 264 PDB 2BBA 2BBA 250 264 SEQADV 2BBA HIS A 12 UNP P54760 EXPRESSION TAG SEQADV 2BBA HIS A 13 UNP P54760 EXPRESSION TAG SEQADV 2BBA HIS A 14 UNP P54760 EXPRESSION TAG SEQADV 2BBA HIS A 15 UNP P54760 EXPRESSION TAG SEQADV 2BBA HIS A 16 UNP P54760 EXPRESSION TAG SEQRES 1 A 185 HIS HIS HIS HIS HIS GLU GLU THR LEU LEU ASN THR LYS SEQRES 2 A 185 LEU GLU THR ALA ASP LEU LYS TRP VAL THR PHE PRO GLN SEQRES 3 A 185 VAL ASP GLY GLN TRP GLU GLU LEU SER GLY LEU ASP GLU SEQRES 4 A 185 GLU GLN HIS SER VAL ARG THR TYR GLU VAL CYS ASP VAL SEQRES 5 A 185 GLN ARG ALA PRO GLY GLN ALA HIS TRP LEU ARG THR GLY SEQRES 6 A 185 TRP VAL PRO ARG ARG GLY ALA VAL HIS VAL TYR ALA THR SEQRES 7 A 185 LEU ARG PHE THR MET LEU GLU CYS LEU SER LEU PRO ARG SEQRES 8 A 185 ALA GLY ARG SER CYS LYS GLU THR PHE THR VAL PHE TYR SEQRES 9 A 185 TYR GLU SER ASP ALA ASP THR ALA THR ALA LEU THR PRO SEQRES 10 A 185 ALA TRP MET GLU ASN PRO TYR ILE LYS VAL ASP THR VAL SEQRES 11 A 185 ALA ALA GLU HIS LEU THR ARG LYS ARG PRO GLY ALA GLU SEQRES 12 A 185 ALA THR GLY LYS VAL ASN VAL LYS THR LEU ARG LEU GLY SEQRES 13 A 185 PRO LEU SER LYS ALA GLY PHE TYR LEU ALA PHE GLN ASP SEQRES 14 A 185 GLN GLY ALA CYS MET ALA LEU LEU SER LEU HIS LEU PHE SEQRES 15 A 185 TYR LYS LYS SEQRES 1 P 15 THR ASN TYR LEU PHE SER PRO ASN GLY PRO ILE ALA ARG SEQRES 2 P 15 ALA TRP HET SO4 A 1 5 HET SO4 A 2 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *223(H2 O) HELIX 1 1 LYS A 24 GLU A 26 5 3 HELIX 2 2 GLU A 96 LEU A 100 5 5 HELIX 3 3 ILE P 260 TRP P 264 5 5 SHEET 1 A 4 HIS A 16 ASN A 22 0 SHEET 2 A 4 CYS A 184 LYS A 196 -1 O LYS A 196 N HIS A 16 SHEET 3 A 4 SER A 54 CYS A 61 -1 N TYR A 58 O LEU A 187 SHEET 4 A 4 GLU A 43 LEU A 48 -1 N GLY A 47 O VAL A 55 SHEET 1 B 4 HIS A 16 ASN A 22 0 SHEET 2 B 4 CYS A 184 LYS A 196 -1 O LYS A 196 N HIS A 16 SHEET 3 B 4 VAL A 86 MET A 94 -1 N TYR A 87 O PHE A 193 SHEET 4 B 4 ASN A 160 LEU A 166 -1 O LEU A 166 N VAL A 86 SHEET 1 C 4 VAL A 33 PHE A 35 0 SHEET 2 C 4 ALA A 70 ARG A 74 -1 O TRP A 72 N PHE A 35 SHEET 3 C 4 GLY A 173 GLN A 181 -1 O PHE A 178 N LEU A 73 SHEET 4 C 4 VAL A 78 PRO A 79 -1 N VAL A 78 O PHE A 174 SHEET 1 D 5 VAL A 33 PHE A 35 0 SHEET 2 D 5 ALA A 70 ARG A 74 -1 O TRP A 72 N PHE A 35 SHEET 3 D 5 GLY A 173 GLN A 181 -1 O PHE A 178 N LEU A 73 SHEET 4 D 5 THR A 110 SER A 118 -1 N PHE A 114 O ALA A 177 SHEET 5 D 5 ILE A 136 ALA A 142 -1 O ILE A 136 N TYR A 115 SSBOND 1 CYS A 61 CYS A 184 1555 1555 2.07 SSBOND 2 CYS A 97 CYS A 107 1555 1555 2.07 CISPEP 1 PHE A 35 PRO A 36 0 -1.49 CISPEP 2 THR A 127 PRO A 128 0 -8.05 CISPEP 3 ASN A 133 PRO A 134 0 20.98 CISPEP 4 GLY A 167 PRO A 168 0 3.52 SITE 1 AC1 7 LYS A 24 THR A 89 ARG A 91 PRO A 134 SITE 2 AC1 7 HIS A 191 HOH A 309 HOH A 318 SITE 1 AC2 5 HIS A 145 LYS A 158 HOH A 330 HOH A 349 SITE 2 AC2 5 HOH A 544 CRYST1 60.972 60.972 151.681 90.00 90.00 90.00 P 41 21 2 8 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 0.016401 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016401 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006593 0.00000