PDB Short entry for 3KR3 HEADER IMMUNE SYSTEM 17-NOV-09 3KR3 TITLE CRYSTAL STRUCTURE OF IGF-II ANTIBODY COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: INSULIN-LIKE GROWTH FACTOR II; COMPND 3 CHAIN: D; COMPND 4 SYNONYM: IGF-II, SOMATOMEDIN-A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: ANTIBODY-FAB (HEAVY CHAIN); COMPND 8 CHAIN: H; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: ANTIBODY-FAB (LIGHT CHAIN); COMPND 12 CHAIN: L; COMPND 13 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: IGF-II, IGF2, PP1446; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: NOVOZYME PROPRIETARY; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 EXPRESSION_SYSTEM_VECTOR: PHAGEMID VECTOR PMID21; SOURCE 16 MOL_ID: 3; SOURCE 17 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 18 ORGANISM_COMMON: HUMAN; SOURCE 19 ORGANISM_TAXID: 9606; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 22 EXPRESSION_SYSTEM_VECTOR: PHAGEMID VECTOR PMID21 KEYWDS ANTIBODY-TARGET COMPLEX, CARBOHYDRATE METABOLISM, GLUCOSE METABOLISM, KEYWDS 2 GLYCOPROTEIN, GROWTH FACTOR, HORMONE, MITOGEN, OSTEOGENESIS, KEYWDS 3 SECRETED, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR T.S.PEAT,J.NEWMAN,T.E.ADAMS REVDAT 3 07-JUL-10 3KR3 1 JRNL REVDAT 2 23-JUN-10 3KR3 1 SOURCE REVDAT 1 16-JUN-10 3KR3 0 JRNL AUTH D.T.DRANSFIELD,E.H.COHEN,Q.CHANG,L.G.SPARROW,J.D.BENTLEY, JRNL AUTH 2 O.DOLEZAL,X.XIAO,T.S.PEAT,J.NEWMAN,P.A.PILLING,T.PHAN, JRNL AUTH 3 I.PRIEBE,G.V.BRIERLEY,N.KASTRAPELI,K.KOPACZ,D.MARTIK, JRNL AUTH 4 D.WASSAF,D.RANK,G.CONLEY,Y.HUANG,T.E.ADAMS,L.COSGROVE JRNL TITL A HUMAN MONOCLONAL ANTIBODY AGAINST INSULIN-LIKE GROWTH JRNL TITL 2 FACTOR-II BLOCKS THE GROWTH OF HUMAN HEPATOCELLULAR JRNL TITL 3 CARCINOMA CELL LINES IN VITRO AND IN VIVO. JRNL REF MOL.CANCER THER. V. 9 1809 2010 JRNL REFN ISSN 1535-7163 JRNL PMID 20515953 JRNL DOI 10.1158/1535-7163.MCT-09-1134 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.6 REMARK 3 NUMBER OF REFLECTIONS : 26600 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1421 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1934 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.2340 REMARK 3 BIN FREE R VALUE SET COUNT : 104 REMARK 3 BIN FREE R VALUE : 0.3160 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3732 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 194 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.66000 REMARK 3 B22 (A**2) : -1.29000 REMARK 3 B33 (A**2) : -1.37000 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): 0.285 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.226 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.151 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.886 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3902 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5308 ; 1.780 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 506 ; 7.117 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 159 ;32.867 ;24.151 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 633 ;16.977 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;19.733 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 594 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2950 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1761 ; 0.219 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2651 ; 0.303 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 257 ; 0.188 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL 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): 41 ; 0.195 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.113 ; 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): 2532 ; 0.958 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4014 ; 1.655 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1565 ; 2.433 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1287 ; 3.461 ; 4.500 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 3KR3 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JAN-10. REMARK 100 THE RCSB ID CODE IS RCSB056341. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAY-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.95363 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26600 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 37.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.6 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) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.8 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18.5% PEG 6000, 118MM CACL2, 10% (V/V) REMARK 280 PCB BUFFER (PROPIONATE-CACODYLATE-BIS-TRIS PROPANE BUFFER), PH REMARK 280 5.3, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 25.33350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.32850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.46050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.32850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.33350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.46050 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, H, L 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 ALA D 1 REMARK 465 TYR D 2 REMARK 465 ARG D 3 REMARK 465 PRO D 4 REMARK 465 LYS D 65 REMARK 465 SER D 66 REMARK 465 GLU D 67 REMARK 465 LYS H 138 REMARK 465 SER H 139 REMARK 465 THR H 140 REMARK 465 SER H 141 REMARK 465 GLY H 142 REMARK 465 SER H 224 REMARK 465 CYS H 225 REMARK 465 ALA H 226 REMARK 465 ALA H 227 REMARK 465 ALA H 228 REMARK 465 HIS H 229 REMARK 465 HIS H 230 REMARK 465 HIS H 231 REMARK 465 HIS H 232 REMARK 465 HIS H 233 REMARK 465 HIS H 234 REMARK 465 GLY H 235 REMARK 465 ALA H 236 REMARK 465 ALA H 237 REMARK 465 GLU H 238 REMARK 465 GLN H 239 REMARK 465 LYS H 240 REMARK 465 LEU H 241 REMARK 465 ILE H 242 REMARK 465 SER H 243 REMARK 465 GLU H 244 REMARK 465 GLU H 245 REMARK 465 ASP H 246 REMARK 465 LEU H 247 REMARK 465 ASN H 248 REMARK 465 GLY H 249 REMARK 465 ALA H 250 REMARK 465 ALA H 251 REMARK 465 CYS L 215 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 H 223 CG CD CE NZ REMARK 470 GLU L 214 CG CD OE1 OE2 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 O PRO L 41 O HOH L 270 1.89 REMARK 500 O ARG L 109 O HOH L 301 1.99 REMARK 500 OE1 GLU L 196 O HOH L 310 2.06 REMARK 500 OE1 GLU H 157 O HOH H 275 2.06 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 LEU H 187 CA - CB - CG ANGL. DEV. = 16.4 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 H 92 169.46 179.96 REMARK 500 VAL H 104 78.28 73.77 REMARK 500 SER H 136 -151.66 -141.72 REMARK 500 ASP H 153 57.00 71.35 REMARK 500 LEU H 198 18.82 -152.04 REMARK 500 PRO H 211 -14.56 -49.27 REMARK 500 SER L 31 -137.75 54.56 REMARK 500 ALA L 52 -42.67 73.84 REMARK 500 THR L 70 57.14 -100.66 REMARK 500 SER L 78 61.99 65.47 REMARK 500 PRO L 96 33.07 -97.75 REMARK 500 LYS L 127 -39.57 -37.51 REMARK 500 ASN L 153 -0.97 76.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ARG D 49 24.8 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH H 314 DISTANCE = 5.08 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO H 252 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO H 253 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO H 254 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO L 216 DBREF 3KR3 D 1 67 UNP P01344 IGF2_HUMAN 25 91 DBREF 3KR3 H 1 251 PDB 3KR3 3KR3 1 251 DBREF 3KR3 L 1 215 PDB 3KR3 3KR3 1 215 SEQRES 1 D 67 ALA TYR ARG PRO SER GLU THR LEU CYS GLY GLY GLU LEU SEQRES 2 D 67 VAL ASP THR LEU GLN PHE VAL CYS GLY ASP ARG GLY PHE SEQRES 3 D 67 TYR PHE SER ARG PRO ALA SER ARG VAL SER ARG ARG SER SEQRES 4 D 67 ARG GLY ILE VAL GLU GLU CYS CYS PHE ARG SER CYS ASP SEQRES 5 D 67 LEU ALA LEU LEU GLU THR TYR CYS ALA THR PRO ALA LYS SEQRES 6 D 67 SER GLU SEQRES 1 H 251 GLU VAL GLN LEU LEU GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 H 251 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 251 PHE THR PHE SER ASN TYR ILE MET TRP TRP VAL ARG GLN SEQRES 4 H 251 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER VAL ILE SER SEQRES 5 H 251 SER SER GLY GLY MET THR ARG TYR ALA ASP SER VAL LYS SEQRES 6 H 251 GLY ARG PHE THR ILE SER ARG ASP ASN SER LYS ASN THR SEQRES 7 H 251 LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 H 251 ALA VAL TYR TYR CYS ALA ARG ASP ASN GLY ASP TYR VAL SEQRES 9 H 251 GLY GLU LYS GLY PHE ASP ILE TRP GLY GLN GLY THR MET SEQRES 10 H 251 VAL THR VAL SER SER ALA SER THR LYS GLY PRO SER VAL SEQRES 11 H 251 PHE PRO LEU ALA PRO SER SER LYS SER THR SER GLY GLY SEQRES 12 H 251 THR ALA ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO SEQRES 13 H 251 GLU PRO VAL THR VAL SER TRP ASN SER GLY ALA LEU THR SEQRES 14 H 251 SER GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SER SER SEQRES 15 H 251 GLY LEU TYR SER LEU SER SER VAL VAL THR VAL PRO SER SEQRES 16 H 251 SER SER LEU GLY THR GLN THR TYR ILE CYS ASN VAL ASN SEQRES 17 H 251 HIS LYS PRO SER ASN THR LYS VAL ASP LYS LYS VAL GLU SEQRES 18 H 251 PRO LYS SER CYS ALA ALA ALA HIS HIS HIS HIS HIS HIS SEQRES 19 H 251 GLY ALA ALA GLU GLN LYS LEU ILE SER GLU GLU ASP LEU SEQRES 20 H 251 ASN GLY ALA ALA SEQRES 1 L 215 GLN ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER SEQRES 2 L 215 ALA SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SEQRES 3 L 215 SER GLN SER ILE SER ASN TYR LEU ASN TRP TYR GLN GLN SEQRES 4 L 215 LYS PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR THR ALA SEQRES 5 L 215 SER THR LEU GLN SER GLY VAL PRO SER ARG PHE SER GLY SEQRES 6 L 215 SER ALA SER GLY THR ASP PHE THR LEU THR ILE ASN SER SEQRES 7 L 215 LEU GLN PRO GLU ASP PHE ALA THR TYR SER CYS GLN GLN SEQRES 8 L 215 SER TYR ASN SER PRO TRP THR PHE GLY GLN GLY THR LYS SEQRES 9 L 215 VAL GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE SEQRES 10 L 215 ILE PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR SEQRES 11 L 215 ALA SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG SEQRES 12 L 215 GLU ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SEQRES 13 L 215 SER GLY ASN SER GLN GLU SER VAL THR GLN GLU ASP SER SEQRES 14 L 215 LYS ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SEQRES 15 L 215 SER LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS SEQRES 16 L 215 GLU VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SEQRES 17 L 215 SER PHE ASN ARG GLY GLU CYS HET EDO H 252 4 HET EDO H 253 4 HET EDO H 254 4 HET EDO L 216 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 4 EDO 4(C2 H6 O2) FORMUL 8 HOH *194(H2 O) HELIX 1 1 CYS D 9 CYS D 21 1 13 HELIX 2 2 ARG D 30 VAL D 35 1 6 HELIX 3 3 SER D 36 ARG D 49 1 14 HELIX 4 4 ASP D 52 TYR D 59 1 8 HELIX 5 5 THR H 28 TYR H 32 5 5 HELIX 6 6 ASP H 62 LYS H 65 5 4 HELIX 7 7 ARG H 87 THR H 91 5 5 HELIX 8 8 SER H 165 ALA H 167 5 3 HELIX 9 9 LYS H 210 ASN H 213 5 4 HELIX 10 10 GLN L 80 PHE L 84 5 5 HELIX 11 11 SER L 122 SER L 128 1 7 HELIX 12 12 LYS L 184 LYS L 189 1 6 SHEET 1 A 4 GLN H 3 SER H 7 0 SHEET 2 A 4 LEU H 18 SER H 25 -1 O ALA H 23 N LEU H 5 SHEET 3 A 4 THR H 78 MET H 83 -1 O MET H 83 N LEU H 18 SHEET 4 A 4 PHE H 68 ASP H 73 -1 N THR H 69 O GLN H 82 SHEET 1 B 6 GLY H 10 VAL H 12 0 SHEET 2 B 6 THR H 116 VAL H 120 1 O THR H 119 N GLY H 10 SHEET 3 B 6 ALA H 92 ASP H 99 -1 N TYR H 94 O THR H 116 SHEET 4 B 6 MET H 34 GLN H 39 -1 N VAL H 37 O TYR H 95 SHEET 5 B 6 LEU H 45 ILE H 51 -1 O VAL H 48 N TRP H 36 SHEET 6 B 6 THR H 58 TYR H 60 -1 O ARG H 59 N VAL H 50 SHEET 1 C 4 GLY H 10 VAL H 12 0 SHEET 2 C 4 THR H 116 VAL H 120 1 O THR H 119 N GLY H 10 SHEET 3 C 4 ALA H 92 ASP H 99 -1 N TYR H 94 O THR H 116 SHEET 4 C 4 PHE H 109 TRP H 112 -1 O ILE H 111 N ARG H 98 SHEET 1 D 4 SER H 129 LEU H 133 0 SHEET 2 D 4 THR H 144 TYR H 154 -1 O LYS H 152 N SER H 129 SHEET 3 D 4 TYR H 185 PRO H 194 -1 O LEU H 187 N VAL H 151 SHEET 4 D 4 VAL H 172 THR H 174 -1 N HIS H 173 O VAL H 190 SHEET 1 E 4 SER H 129 LEU H 133 0 SHEET 2 E 4 THR H 144 TYR H 154 -1 O LYS H 152 N SER H 129 SHEET 3 E 4 TYR H 185 PRO H 194 -1 O LEU H 187 N VAL H 151 SHEET 4 E 4 VAL H 178 LEU H 179 -1 N VAL H 178 O SER H 186 SHEET 1 F 3 THR H 160 TRP H 163 0 SHEET 2 F 3 ILE H 204 HIS H 209 -1 O ASN H 206 N SER H 162 SHEET 3 F 3 THR H 214 LYS H 219 -1 O VAL H 216 N VAL H 207 SHEET 1 G 4 MET L 5 SER L 8 0 SHEET 2 G 4 VAL L 20 ALA L 26 -1 O ARG L 25 N THR L 6 SHEET 3 G 4 PHE L 72 ILE L 76 -1 O LEU L 74 N ILE L 22 SHEET 4 G 4 PHE L 63 ALA L 67 -1 N SER L 64 O THR L 75 SHEET 1 H 6 SER L 11 SER L 15 0 SHEET 2 H 6 THR L 103 LYS L 108 1 O GLU L 106 N LEU L 12 SHEET 3 H 6 ALA L 85 GLN L 91 -1 N TYR L 87 O THR L 103 SHEET 4 H 6 LEU L 34 GLN L 39 -1 N GLN L 39 O THR L 86 SHEET 5 H 6 LYS L 46 TYR L 50 -1 O LEU L 48 N TRP L 36 SHEET 6 H 6 THR L 54 LEU L 55 -1 O THR L 54 N TYR L 50 SHEET 1 I 4 SER L 115 PHE L 119 0 SHEET 2 I 4 THR L 130 PHE L 140 -1 O ASN L 138 N SER L 115 SHEET 3 I 4 TYR L 174 SER L 183 -1 O LEU L 182 N ALA L 131 SHEET 4 I 4 SER L 160 VAL L 164 -1 N SER L 163 O SER L 177 SHEET 1 J 4 ALA L 154 LEU L 155 0 SHEET 2 J 4 LYS L 146 VAL L 151 -1 N VAL L 151 O ALA L 154 SHEET 3 J 4 VAL L 192 THR L 198 -1 O GLU L 196 N GLN L 148 SHEET 4 J 4 VAL L 206 ASN L 211 -1 O VAL L 206 N VAL L 197 SSBOND 1 CYS D 9 CYS D 47 1555 1555 2.05 SSBOND 2 CYS D 21 CYS D 60 1555 1555 2.01 SSBOND 3 CYS D 46 CYS D 51 1555 1555 2.04 SSBOND 4 CYS H 22 CYS H 96 1555 1555 2.06 SSBOND 5 CYS H 149 CYS H 205 1555 1555 2.05 SSBOND 6 CYS L 24 CYS L 89 1555 1555 2.04 SSBOND 7 CYS L 135 CYS L 195 1555 1555 2.00 CISPEP 1 PHE H 155 PRO H 156 0 -3.84 CISPEP 2 GLU H 157 PRO H 158 0 -5.74 CISPEP 3 SER L 8 PRO L 9 0 -4.61 CISPEP 4 SER L 95 PRO L 96 0 5.25 CISPEP 5 TYR L 141 PRO L 142 0 -2.19 SITE 1 AC1 5 VAL D 35 ARG D 40 SER H 30 ASN H 31 SITE 2 AC1 5 SER H 53 SITE 1 AC2 6 LEU H 150 SER H 186 LEU H 187 SER H 188 SITE 2 AC2 6 THR L 179 HOH L 255 SITE 1 AC3 10 GLY H 9 GLY H 10 MET H 117 THR H 119 SITE 2 AC3 10 PRO H 156 GLU H 157 PRO H 158 PRO H 211 SITE 3 AC3 10 HOH H 256 HOH H 320 SITE 1 AC4 6 PRO L 81 ARG L 109 ASP L 171 SER L 172 SITE 2 AC4 6 HOH L 291 HOH L 296 CRYST1 50.667 106.921 110.657 90.00 90.00 90.00 P 21 21 21 4 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 0.019737 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009353 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009037 0.00000