PDB Short entry for 1GP9 HEADER HORMONE/GROWTH FACTOR 31-OCT-01 1GP9 TITLE A NEW CRYSTAL FORM OF THE NK1 SPLICE VARIANT OF HGF/SF DEMONSTRATES TITLE 2 EXTENSIVE HINGE MOVEMENT AND SUGGESTS THAT THE NK1 DIMER ORIGINATES TITLE 3 BY DOMAIN SWAPPING COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEPATOCYTE GROWTH FACTOR; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: NK1, RESIDUES 40-210; COMPND 5 SYNONYM: SCATTER FACTOR, SF, HEPATOPOEITIN A; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL: FIBROBLAST; SOURCE 6 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: GS115; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PPIC-9K; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPIC-9K KEYWDS HORMONE/GROWTH FACTOR, HGF/SF, NK1, MET, DOMAIN SWAPPING, PROTEIN KEYWDS 2 ENGINEERING, GROWTH FACTOR, KRINGLE, GLYCOPROTEIN, HORMONE-GROWTH KEYWDS 3 FACTOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.WATANABE,D.Y.CHIRGADZE,D.LIETHA,E.GHERARDI,T.L.BLUNDELL REVDAT 6 13-DEC-23 1GP9 1 REMARK REVDAT 5 08-NOV-17 1GP9 1 TITLE SOURCE ATOM REVDAT 4 24-FEB-09 1GP9 1 VERSN REVDAT 3 24-JUN-03 1GP9 1 ATOM TER HETATM CONECT REVDAT 2 13-JUN-02 1GP9 1 JRNL REVDAT 1 19-NOV-01 1GP9 0 JRNL AUTH K.WATANABE,D.Y.CHIRGADZE,D.LIETHA,H.DE JONGE,T.L.BLUNDELL, JRNL AUTH 2 E.GHERARDI JRNL TITL A NEW CRYSTAL FORM OF THE NK1 SPLICE VARIANT OF HGF/SF JRNL TITL 2 DEMONSTRATES EXTENSIVE HINGE MOVEMENT AND SUGGESTS THAT THE JRNL TITL 3 NK1 DIMER ORIGINATES BY DOMAIN SWAPPING JRNL REF J.MOL.BIOL. V. 319 283 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 12051906 JRNL DOI 10.1016/S0022-2836(02)00199-7 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 28444 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 SET) : 0.237 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1420 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4615 REMARK 3 BIN R VALUE (WORKING SET) : 0.3360 REMARK 3 BIN FREE R VALUE : 0.4780 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 243 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.031 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5463 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 75 REMARK 3 SOLVENT ATOMS : 156 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.83000 REMARK 3 B22 (A**2) : 7.59000 REMARK 3 B33 (A**2) : -1.76000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.37 REMARK 3 ESD FROM SIGMAA (A) : 0.33 REMARK 3 LOW RESOLUTION CUTOFF (A) : 20.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.52 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.55 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.060 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 3.410 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.250 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.600 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.360 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT REMARK 3 KSOL : 0.32 REMARK 3 BSOL : 47.20 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : EPE.PAR REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : EPE.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 1GP9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-OCT-01. REMARK 100 THE DEPOSITION ID IS D_1290008626. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-SEP-98 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX7.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.488 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33095 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.440 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 200 DATA REDUNDANCY : 12.80 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.35200 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: PDB ENTRIES 1NK1 1BHT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG4000, 10% 2-PROPANOL, 0.1M REMARK 280 SODIUM HEPES, PH 7.5, PH 7.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z 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 152.23000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 152.23000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 36.74000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.13000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 36.74000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.13000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 152.23000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 36.74000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 39.13000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 152.23000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 36.74000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 39.13000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, 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 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 GLU A 34 REMARK 465 ALA A 35 REMARK 465 GLU A 36 REMARK 465 ALA A 37 REMARK 465 TYR A 38 REMARK 465 VAL A 209 REMARK 465 GLU A 210 REMARK 465 GLU B 34 REMARK 465 ALA B 35 REMARK 465 GLU B 36 REMARK 465 ALA B 37 REMARK 465 TYR B 38 REMARK 465 VAL B 209 REMARK 465 GLU B 210 REMARK 465 GLU C 34 REMARK 465 ALA C 35 REMARK 465 GLU C 36 REMARK 465 ALA C 37 REMARK 465 VAL C 209 REMARK 465 GLU C 210 REMARK 465 GLU D 34 REMARK 465 ALA D 35 REMARK 465 GLU D 36 REMARK 465 ALA D 37 REMARK 465 TYR D 38 REMARK 465 VAL D 209 REMARK 465 GLU D 210 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 ASP D 68 CG OD1 OD2 REMARK 470 ARG D 76 CG CD NE CZ NH1 NH2 REMARK 470 ARG D 93 NE CZ NH1 NH2 REMARK 470 LYS D 122 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 CD2 HIS D 160 O HOH D 2026 0.62 REMARK 500 CA SER D 192 O HOH D 2035 0.65 REMARK 500 CG HIS D 160 O HOH D 2026 0.87 REMARK 500 N SER D 192 O HOH D 2035 1.01 REMARK 500 NE2 HIS D 160 O HOH D 2026 1.51 REMARK 500 C SER D 192 O HOH D 2035 1.64 REMARK 500 ND1 HIS D 160 O HOH D 2026 1.69 REMARK 500 C THR D 191 O HOH D 2035 1.80 REMARK 500 ND1 HIS D 160 O HOH D 2025 1.92 REMARK 500 CE1 HIS D 160 O HOH D 2026 1.95 REMARK 500 O PRO A 164 O TYR A 167 2.02 REMARK 500 CE1 HIS D 160 O HOH D 2025 2.04 REMARK 500 CB SER D 192 O HOH D 2035 2.11 REMARK 500 N GLY B 169 O2S EPE B 1210 2.15 REMARK 500 N ASN D 193 O HOH D 2035 2.17 REMARK 500 O THR D 191 O HOH D 2035 2.18 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 CYS A 96 CA - CB - SG ANGL. DEV. = 7.7 DEGREES REMARK 500 CYS B 128 CA - CB - SG ANGL. DEV. = 7.0 DEGREES REMARK 500 PRO C 180 C - N - CA ANGL. DEV. = 11.2 DEGREES REMARK 500 PRO D 100 C - N - CA ANGL. DEV. = 9.1 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 PRO A 55 -7.00 -55.00 REMARK 500 LYS A 62 -116.48 -146.36 REMARK 500 VAL A 64 -158.07 -156.89 REMARK 500 ASN A 65 -91.33 -113.43 REMARK 500 LYS A 78 -94.95 -36.87 REMARK 500 PRO A 81 13.31 -62.14 REMARK 500 LYS A 91 -5.28 -54.98 REMARK 500 LYS A 94 20.49 32.65 REMARK 500 ASN A 102 -159.31 -131.82 REMARK 500 HIS A 114 -18.44 -49.38 REMARK 500 SER A 135 30.84 -99.45 REMARK 500 SER A 166 -72.61 -57.93 REMARK 500 GLU A 174 -121.55 50.05 REMARK 500 ASP A 202 72.97 -106.58 REMARK 500 ALA B 56 -71.54 -53.64 REMARK 500 LEU B 57 125.67 -30.50 REMARK 500 ASN B 77 48.87 38.29 REMARK 500 PRO B 81 31.37 -70.27 REMARK 500 PHE B 82 172.09 178.83 REMARK 500 ALA B 86 161.24 175.02 REMARK 500 LYS B 94 77.77 63.23 REMARK 500 SER B 103 -9.03 -58.94 REMARK 500 ARG B 126 120.08 -37.04 REMARK 500 LYS B 137 10.87 -140.87 REMARK 500 SER B 141 39.92 -144.07 REMARK 500 GLU B 174 -128.80 50.83 REMARK 500 GLU B 184 2.23 -45.63 REMARK 500 LYS C 62 121.63 -174.90 REMARK 500 LYS C 78 -100.62 -45.62 REMARK 500 PRO C 81 30.41 -72.87 REMARK 500 SER C 103 -35.21 -39.81 REMARK 500 ILE C 156 -78.89 -50.99 REMARK 500 PHE C 162 71.58 -101.52 REMARK 500 TYR C 167 47.50 -109.59 REMARK 500 ASP C 171 56.33 39.83 REMARK 500 GLU C 174 -131.74 45.73 REMARK 500 GLU C 183 150.73 -47.91 REMARK 500 SER C 207 88.34 -69.11 REMARK 500 ASP D 54 77.25 -106.46 REMARK 500 PRO D 55 42.84 -45.43 REMARK 500 PRO D 81 25.83 -56.09 REMARK 500 ASP D 90 79.90 -112.50 REMARK 500 LYS D 137 14.93 -140.41 REMARK 500 SER D 141 38.92 -142.13 REMARK 500 TYR D 167 29.67 -147.40 REMARK 500 GLU D 174 -125.59 50.45 REMARK 500 ARG D 181 -85.48 -93.56 REMARK 500 SER D 207 173.16 157.92 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 TYR C 124 0.07 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 EPE A1209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE B1209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE B1210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE C1209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE D1209 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BHT RELATED DB: PDB REMARK 900 NK1 FRAGMENT OF HUMAN HEPATOCYTE GROWTH FACTOR REMARK 900 RELATED ID: 1GMN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF NK1-HEPARIN COMPLEXES REVEAL THE BASIS FOR REMARK 900 NK1 ACTIVITY AND ENABLE ENGINEERING OF POTENT AGONISTS OF THE MET REMARK 900 RECEPTOR REMARK 900 RELATED ID: 1GMO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF NK1-HEPARIN COMPLEXES REVEAL THE BASIS FOR REMARK 900 NK1 ACTIVITY AND ENABLE ENGINEERING OF POTENT AGONISTS OF THE MET REMARK 900 RECEPTOR REMARK 900 RELATED ID: 1NK1 RELATED DB: PDB REMARK 900 NK1 FRAGMENT OF HUMAN HEPATOCYTE GROWTH FACTOR/SCATTER FACTOR (HGF/ REMARK 900 SF) AT 2.5 ANGSTROM RESOLUTION REMARK 900 RELATED ID: 2HGF RELATED DB: PDB REMARK 900 HAIRPIN LOOP CONTAINING DOMAIN OF HEPATOCYTE GROWTH FACTOR, NMR, REMARK 900 MINIMIZED AVERAGE STRUCTURE DBREF 1GP9 A 34 39 PDB 1GP9 1GP9 34 39 DBREF 1GP9 A 40 210 UNP P14210 P14210 40 210 DBREF 1GP9 B 34 39 PDB 1GP9 1GP9 34 39 DBREF 1GP9 B 40 210 UNP P14210 P14210 40 210 DBREF 1GP9 C 34 39 PDB 1GP9 1GP9 34 39 DBREF 1GP9 C 40 210 UNP P14210 P14210 40 210 DBREF 1GP9 D 34 39 PDB 1GP9 1GP9 34 39 DBREF 1GP9 D 40 210 UNP P14210 P14210 40 210 SEQRES 1 A 177 GLU ALA GLU ALA TYR VAL HIS GLU PHE LYS LYS SER ALA SEQRES 2 A 177 LYS THR THR LEU ILE LYS ILE ASP PRO ALA LEU LYS ILE SEQRES 3 A 177 LYS THR LYS LYS VAL ASN THR ALA ASP GLN CYS ALA ASN SEQRES 4 A 177 ARG CYS THR ARG ASN LYS GLY LEU PRO PHE THR CYS LYS SEQRES 5 A 177 ALA PHE VAL PHE ASP LYS ALA ARG LYS GLN CYS LEU TRP SEQRES 6 A 177 PHE PRO PHE ASN SER MET SER SER GLY VAL LYS LYS GLU SEQRES 7 A 177 PHE GLY HIS GLU PHE ASP LEU TYR GLU ASN LYS ASP TYR SEQRES 8 A 177 ILE ARG ASN CYS ILE ILE GLY LYS GLY ARG SER TYR LYS SEQRES 9 A 177 GLY THR VAL SER ILE THR LYS SER GLY ILE LYS CYS GLN SEQRES 10 A 177 PRO TRP SER SER MET ILE PRO HIS GLU HIS SER PHE LEU SEQRES 11 A 177 PRO SER SER TYR ARG GLY LYS ASP LEU GLN GLU ASN TYR SEQRES 12 A 177 CYS ARG ASN PRO ARG GLY GLU GLU GLY GLY PRO TRP CYS SEQRES 13 A 177 PHE THR SER ASN PRO GLU VAL ARG TYR GLU VAL CYS ASP SEQRES 14 A 177 ILE PRO GLN CYS SER GLU VAL GLU SEQRES 1 B 177 GLU ALA GLU ALA TYR VAL HIS GLU PHE LYS LYS SER ALA SEQRES 2 B 177 LYS THR THR LEU ILE LYS ILE ASP PRO ALA LEU LYS ILE SEQRES 3 B 177 LYS THR LYS LYS VAL ASN THR ALA ASP GLN CYS ALA ASN SEQRES 4 B 177 ARG CYS THR ARG ASN LYS GLY LEU PRO PHE THR CYS LYS SEQRES 5 B 177 ALA PHE VAL PHE ASP LYS ALA ARG LYS GLN CYS LEU TRP SEQRES 6 B 177 PHE PRO PHE ASN SER MET SER SER GLY VAL LYS LYS GLU SEQRES 7 B 177 PHE GLY HIS GLU PHE ASP LEU TYR GLU ASN LYS ASP TYR SEQRES 8 B 177 ILE ARG ASN CYS ILE ILE GLY LYS GLY ARG SER TYR LYS SEQRES 9 B 177 GLY THR VAL SER ILE THR LYS SER GLY ILE LYS CYS GLN SEQRES 10 B 177 PRO TRP SER SER MET ILE PRO HIS GLU HIS SER PHE LEU SEQRES 11 B 177 PRO SER SER TYR ARG GLY LYS ASP LEU GLN GLU ASN TYR SEQRES 12 B 177 CYS ARG ASN PRO ARG GLY GLU GLU GLY GLY PRO TRP CYS SEQRES 13 B 177 PHE THR SER ASN PRO GLU VAL ARG TYR GLU VAL CYS ASP SEQRES 14 B 177 ILE PRO GLN CYS SER GLU VAL GLU SEQRES 1 C 177 GLU ALA GLU ALA TYR VAL HIS GLU PHE LYS LYS SER ALA SEQRES 2 C 177 LYS THR THR LEU ILE LYS ILE ASP PRO ALA LEU LYS ILE SEQRES 3 C 177 LYS THR LYS LYS VAL ASN THR ALA ASP GLN CYS ALA ASN SEQRES 4 C 177 ARG CYS THR ARG ASN LYS GLY LEU PRO PHE THR CYS LYS SEQRES 5 C 177 ALA PHE VAL PHE ASP LYS ALA ARG LYS GLN CYS LEU TRP SEQRES 6 C 177 PHE PRO PHE ASN SER MET SER SER GLY VAL LYS LYS GLU SEQRES 7 C 177 PHE GLY HIS GLU PHE ASP LEU TYR GLU ASN LYS ASP TYR SEQRES 8 C 177 ILE ARG ASN CYS ILE ILE GLY LYS GLY ARG SER TYR LYS SEQRES 9 C 177 GLY THR VAL SER ILE THR LYS SER GLY ILE LYS CYS GLN SEQRES 10 C 177 PRO TRP SER SER MET ILE PRO HIS GLU HIS SER PHE LEU SEQRES 11 C 177 PRO SER SER TYR ARG GLY LYS ASP LEU GLN GLU ASN TYR SEQRES 12 C 177 CYS ARG ASN PRO ARG GLY GLU GLU GLY GLY PRO TRP CYS SEQRES 13 C 177 PHE THR SER ASN PRO GLU VAL ARG TYR GLU VAL CYS ASP SEQRES 14 C 177 ILE PRO GLN CYS SER GLU VAL GLU SEQRES 1 D 177 GLU ALA GLU ALA TYR VAL HIS GLU PHE LYS LYS SER ALA SEQRES 2 D 177 LYS THR THR LEU ILE LYS ILE ASP PRO ALA LEU LYS ILE SEQRES 3 D 177 LYS THR LYS LYS VAL ASN THR ALA ASP GLN CYS ALA ASN SEQRES 4 D 177 ARG CYS THR ARG ASN LYS GLY LEU PRO PHE THR CYS LYS SEQRES 5 D 177 ALA PHE VAL PHE ASP LYS ALA ARG LYS GLN CYS LEU TRP SEQRES 6 D 177 PHE PRO PHE ASN SER MET SER SER GLY VAL LYS LYS GLU SEQRES 7 D 177 PHE GLY HIS GLU PHE ASP LEU TYR GLU ASN LYS ASP TYR SEQRES 8 D 177 ILE ARG ASN CYS ILE ILE GLY LYS GLY ARG SER TYR LYS SEQRES 9 D 177 GLY THR VAL SER ILE THR LYS SER GLY ILE LYS CYS GLN SEQRES 10 D 177 PRO TRP SER SER MET ILE PRO HIS GLU HIS SER PHE LEU SEQRES 11 D 177 PRO SER SER TYR ARG GLY LYS ASP LEU GLN GLU ASN TYR SEQRES 12 D 177 CYS ARG ASN PRO ARG GLY GLU GLU GLY GLY PRO TRP CYS SEQRES 13 D 177 PHE THR SER ASN PRO GLU VAL ARG TYR GLU VAL CYS ASP SEQRES 14 D 177 ILE PRO GLN CYS SER GLU VAL GLU HET EPE A1209 15 HET EPE B1209 15 HET EPE B1210 15 HET EPE C1209 15 HET EPE D1209 15 HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 5 EPE 5(C8 H18 N2 O4 S) FORMUL 10 HOH *156(H2 O) HELIX 1 1 THR A 66 ARG A 76 1 11 HELIX 2 2 ASP A 123 ILE A 125 5 3 HELIX 3 3 THR B 66 ARG B 76 1 11 HELIX 4 4 ASP B 123 ILE B 125 5 3 HELIX 5 5 LEU B 163 TYR B 167 5 5 HELIX 6 6 TYR C 38 HIS C 40 5 3 HELIX 7 7 ALA C 67 ARG C 76 1 10 HELIX 8 8 ASP C 123 ILE C 125 5 3 HELIX 9 9 THR D 66 ASN D 77 1 12 HELIX 10 10 ASP D 123 ILE D 125 5 3 HELIX 11 11 LEU D 163 ARG D 168 1 6 SHEET 1 AA 5 PHE A 42 ILE A 51 0 SHEET 2 AA 5 LYS A 109 ASN A 121 -1 O LYS A 109 N ILE A 51 SHEET 3 AA 5 ALA A 86 ASP A 90 -1 O PHE A 87 N TYR A 119 SHEET 4 AA 5 GLN A 95 PHE A 99 -1 O GLN A 95 N ASP A 90 SHEET 5 AA 5 LYS A 60 THR A 61 -1 O LYS A 60 N TRP A 98 SHEET 1 AB 3 CYS A 149 GLN A 150 0 SHEET 2 AB 3 TRP A 188 THR A 191 -1 O PHE A 190 N GLN A 150 SHEET 3 AB 3 TYR A 198 VAL A 200 -1 O GLU A 199 N CYS A 189 SHEET 1 BA 5 PHE B 42 LYS B 52 0 SHEET 2 BA 5 VAL B 108 ASN B 121 -1 O LYS B 109 N ILE B 51 SHEET 3 BA 5 ALA B 86 ASP B 90 -1 O PHE B 87 N TYR B 119 SHEET 4 BA 5 GLN B 95 PHE B 99 -1 O GLN B 95 N ASP B 90 SHEET 5 BA 5 LYS B 60 LYS B 63 -1 O LYS B 60 N TRP B 98 SHEET 1 BB 2 TRP B 188 PHE B 190 0 SHEET 2 BB 2 TYR B 198 VAL B 200 -1 O GLU B 199 N CYS B 189 SHEET 1 CA 5 PHE C 42 LYS C 52 0 SHEET 2 CA 5 VAL C 108 ASN C 121 -1 O LYS C 109 N ILE C 51 SHEET 3 CA 5 ALA C 86 ASP C 90 -1 O PHE C 87 N TYR C 119 SHEET 4 CA 5 GLN C 95 PHE C 99 -1 O GLN C 95 N ASP C 90 SHEET 5 CA 5 LYS C 60 LYS C 63 -1 O LYS C 60 N TRP C 98 SHEET 1 CB 2 TRP C 188 PHE C 190 0 SHEET 2 CB 2 TYR C 198 VAL C 200 -1 O GLU C 199 N CYS C 189 SHEET 1 DA 5 PHE D 42 LYS D 52 0 SHEET 2 DA 5 VAL D 108 ASN D 121 -1 O LYS D 109 N ILE D 51 SHEET 3 DA 5 ALA D 86 ASP D 90 -1 O PHE D 87 N TYR D 119 SHEET 4 DA 5 GLN D 95 PHE D 99 -1 O GLN D 95 N ASP D 90 SHEET 5 DA 5 LYS D 60 LYS D 63 -1 O LYS D 60 N TRP D 98 SHEET 1 DB 2 TRP D 188 PHE D 190 0 SHEET 2 DB 2 TYR D 198 VAL D 200 -1 O GLU D 199 N CYS D 189 SSBOND 1 CYS A 70 CYS A 96 1555 1555 2.03 SSBOND 2 CYS A 74 CYS A 84 1555 1555 2.05 SSBOND 3 CYS A 128 CYS A 206 1555 1555 2.01 SSBOND 4 CYS A 149 CYS A 189 1555 1555 2.03 SSBOND 5 CYS A 177 CYS A 201 1555 1555 2.02 SSBOND 6 CYS B 70 CYS B 96 1555 1555 2.02 SSBOND 7 CYS B 74 CYS B 84 1555 1555 2.07 SSBOND 8 CYS B 128 CYS B 206 1555 1555 2.03 SSBOND 9 CYS B 149 CYS B 189 1555 1555 2.04 SSBOND 10 CYS B 177 CYS B 201 1555 1555 2.04 SSBOND 11 CYS C 70 CYS C 96 1555 1555 2.03 SSBOND 12 CYS C 74 CYS C 84 1555 1555 2.05 SSBOND 13 CYS C 128 CYS C 206 1555 1555 2.04 SSBOND 14 CYS C 149 CYS C 189 1555 1555 2.02 SSBOND 15 CYS C 177 CYS C 201 1555 1555 2.03 SSBOND 16 CYS D 70 CYS D 96 1555 1555 2.03 SSBOND 17 CYS D 74 CYS D 84 1555 1555 2.06 SSBOND 18 CYS D 128 CYS D 206 1555 1555 2.04 SSBOND 19 CYS D 149 CYS D 189 1555 1555 2.03 SSBOND 20 CYS D 177 CYS D 201 1555 1555 2.02 CISPEP 1 ILE A 156 PRO A 157 0 0.21 CISPEP 2 ILE B 156 PRO B 157 0 -1.44 CISPEP 3 ILE D 156 PRO D 157 0 0.17 SITE 1 AC1 8 PHE A 162 GLU A 183 GLY A 185 GLY A 186 SITE 2 AC1 8 TRP A 188 PHE A 190 ARG A 197 ARG D 134 SITE 1 AC2 8 PHE B 162 GLY B 185 GLY B 186 TRP B 188 SITE 2 AC2 8 PHE B 190 ARG B 197 TYR B 198 VAL B 200 SITE 1 AC3 12 HIS A 114 GLU A 115 ALA B 46 LYS B 47 SITE 2 AC3 12 THR B 48 TYR B 167 ARG B 168 GLY B 169 SITE 3 AC3 12 LYS B 170 ASP B 171 LEU B 172 GLN B 173 SITE 1 AC4 9 THR B 61 LYS B 62 LYS B 63 HIS C 158 SITE 2 AC4 9 GLU C 159 GLU C 183 PHE C 190 TYR C 198 SITE 3 AC4 9 HOH C2047 SITE 1 AC5 7 PHE D 162 GLU D 183 GLY D 185 PHE D 190 SITE 2 AC5 7 ARG D 197 TYR D 198 VAL D 200 CRYST1 73.480 78.260 304.460 90.00 90.00 90.00 C 2 2 21 32 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 0.013609 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012778 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003285 0.00000