HEADER IMMUNE SYSTEM 04-NOV-21 7VUX TITLE COMPLEX STRUCTURE OF PD1 AND 609A-FAB COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROGRAMMED CELL DEATH PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN PD-1,HPD-1; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HEAVY CHAIN OF FAB FRAGMENT; COMPND 8 CHAIN: H; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: LIGHT CHAIN OF FAB FRAGMENT; 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: PDCD1, PD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: MAMMAL ENVIRONMENTAL SAMPLE; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 1092587; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 EXPRESSION_SYSTEM: MAMMAL ENVIRONMENTAL SAMPLE; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 1092587 KEYWDS PD1 FAB COMPLEX, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR H.HUANG,Z.ZHU,J.ZHAO,L.JIANG,H.YANG,L.DENG,X.MENG,J.DING,S.YANG, AUTHOR 2 L.ZHAO,W.XU,X.WANG REVDAT 4 16-OCT-24 7VUX 1 REMARK REVDAT 3 29-NOV-23 7VUX 1 REMARK REVDAT 2 16-MAR-22 7VUX 1 JRNL REVDAT 1 17-NOV-21 7VUX 0 JRNL AUTH J.ZHAO,L.JIANG,H.YANG,L.DENG,X.MENG,J.DING,S.YANG,L.ZHAO, JRNL AUTH 2 W.XU,X.WANG,Z.ZHU,H.HUANG JRNL TITL A STRATEGY FOR THE EFFICIENT CONSTRUCTION OF ANTI-PD1-BASED JRNL TITL 2 BISPECIFIC ANTIBODIES WITH DESIRED IGG-LIKE PROPERTIES. JRNL REF MABS V. 14 44435 2022 JRNL REFN ESSN 1942-0870 JRNL PMID 35239451 JRNL DOI 10.1080/19420862.2022.2044435 REMARK 2 REMARK 2 RESOLUTION. 1.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 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) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 67222 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) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3529 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) : 1.64 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.68 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4947 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.87 REMARK 3 BIN R VALUE (WORKING SET) : 0.4070 REMARK 3 BIN FREE R VALUE SET COUNT : 263 REMARK 3 BIN FREE R VALUE : 0.4530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4227 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 88 REMARK 3 SOLVENT ATOMS : 789 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.74000 REMARK 3 B22 (A**2) : -0.07000 REMARK 3 B33 (A**2) : -0.50000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.43000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.092 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.096 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.065 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.959 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4751 ; 0.013 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 4238 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6492 ; 1.784 ; 1.647 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9907 ; 1.472 ; 1.572 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 647 ;20.713 ; 5.402 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 216 ;31.292 ;21.435 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 735 ;12.235 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;17.831 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 615 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6281 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1028 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 7VUX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1300025420. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAY-20 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70749 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 48.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.45700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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: 5WT9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM FORMATE, PH 6.6, 20% REMARK 280 W/V PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 34.20500 REMARK 290 SMTRY3 2 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: 9290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 THR A 153 REMARK 465 ALA A 154 REMARK 465 HIS A 155 REMARK 465 PRO A 156 REMARK 465 SER A 157 REMARK 465 PRO A 158 REMARK 465 SER A 159 REMARK 465 PRO A 160 REMARK 465 GLU A 161 REMARK 465 ASN A 162 REMARK 465 LEU A 163 REMARK 465 TYR A 164 REMARK 465 PHE A 165 REMARK 465 GLN A 166 REMARK 465 CYS L 214 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 OG SER L 202 O HOH L 401 1.54 REMARK 500 MG MG L 307 O HOH L 405 1.57 REMARK 500 O HOH L 422 O HOH L 615 1.60 REMARK 500 C PRO A 152 N THR A 201 1.61 REMARK 500 O HOH H 483 O HOH H 595 1.67 REMARK 500 O HOH A 343 O HOH A 458 1.83 REMARK 500 OE1 GLN A 91 O HOH A 301 1.90 REMARK 500 O HOH A 362 O HOH A 417 1.91 REMARK 500 OG SER L 28 O HOH L 402 1.93 REMARK 500 O HOH H 410 O HOH H 519 1.97 REMARK 500 O HOH H 406 O HOH H 550 2.01 REMARK 500 OG SER H 136 O HOH H 401 2.02 REMARK 500 O3 GOL A 203 O HOH A 302 2.03 REMARK 500 O HOH L 666 O HOH L 682 2.07 REMARK 500 O HOH H 496 O HOH L 616 2.11 REMARK 500 O HOH H 486 O HOH H 647 2.12 REMARK 500 O HOH L 655 O HOH L 724 2.12 REMARK 500 O HOH H 595 O HOH L 540 2.12 REMARK 500 O HOH L 687 O HOH L 701 2.13 REMARK 500 O HOH A 448 O HOH A 469 2.13 REMARK 500 O HOH L 651 O HOH L 669 2.18 REMARK 500 O HOH H 505 O HOH H 638 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH H 531 O HOH H 583 2645 2.01 REMARK 500 O HOH A 460 O HOH H 550 1455 2.03 REMARK 500 O HOH L 685 O HOH L 715 1455 2.05 REMARK 500 O HOH L 634 O HOH L 691 1455 2.11 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 ARG A 104 NE - CZ - NH1 ANGL. DEV. = 3.6 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 THR H 195 -93.37 -64.96 REMARK 500 SER L 30 -126.56 49.76 REMARK 500 SER L 30 -117.69 60.66 REMARK 500 ALA L 51 -43.44 73.12 REMARK 500 ASN L 152 -12.71 77.23 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 A 504 DISTANCE = 6.21 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG H 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 464 O REMARK 620 2 ASP H 105 O 132.9 REMARK 620 3 HOH L 587 O 124.0 93.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG L 307 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 EDO H 307 O1 REMARK 620 2 GLN L 160 O 98.3 REMARK 620 3 SER L 176 O 146.2 90.1 REMARK 620 4 SER L 176 OG 115.5 137.6 47.6 REMARK 620 5 THR L 178 OG1 91.2 93.5 121.1 109.6 REMARK 620 N 1 2 3 4 DBREF 7VUX A 32 160 UNP Q15116 PDCD1_HUMAN 32 160 DBREF 7VUX H 1 216 PDB 7VUX 7VUX 1 216 DBREF 7VUX L 1 214 PDB 7VUX 7VUX 1 214 SEQADV 7VUX MET A 31 UNP Q15116 INITIATING METHIONINE SEQADV 7VUX SER A 93 UNP Q15116 CYS 93 CONFLICT SEQADV 7VUX GLU A 161 UNP Q15116 EXPRESSION TAG SEQADV 7VUX ASN A 162 UNP Q15116 EXPRESSION TAG SEQADV 7VUX LEU A 163 UNP Q15116 EXPRESSION TAG SEQADV 7VUX TYR A 164 UNP Q15116 EXPRESSION TAG SEQADV 7VUX PHE A 165 UNP Q15116 EXPRESSION TAG SEQADV 7VUX GLN A 166 UNP Q15116 EXPRESSION TAG SEQRES 1 A 136 MET TRP ASN PRO PRO THR PHE SER PRO ALA LEU LEU VAL SEQRES 2 A 136 VAL THR GLU GLY ASP ASN ALA THR PHE THR CYS SER PHE SEQRES 3 A 136 SER ASN THR SER GLU SER PHE VAL LEU ASN TRP TYR ARG SEQRES 4 A 136 MET SER PRO SER ASN GLN THR ASP LYS LEU ALA ALA PHE SEQRES 5 A 136 PRO GLU ASP ARG SER GLN PRO GLY GLN ASP SER ARG PHE SEQRES 6 A 136 ARG VAL THR GLN LEU PRO ASN GLY ARG ASP PHE HIS MET SEQRES 7 A 136 SER VAL VAL ARG ALA ARG ARG ASN ASP SER GLY THR TYR SEQRES 8 A 136 LEU CYS GLY ALA ILE SER LEU ALA PRO LYS ALA GLN ILE SEQRES 9 A 136 LYS GLU SER LEU ARG ALA GLU LEU ARG VAL THR GLU ARG SEQRES 10 A 136 ARG ALA GLU VAL PRO THR ALA HIS PRO SER PRO SER PRO SEQRES 11 A 136 GLU ASN LEU TYR PHE GLN SEQRES 1 H 216 GLU VAL LYS LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 H 216 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 216 PHE ALA PHE SER SER TYR ASP MET SER TRP VAL ARG GLN SEQRES 4 H 216 ALA PRO GLY LYS ARG LEU GLU TRP VAL ALA THR ILE SER SEQRES 5 H 216 GLY GLY GLY ARG TYR THR TYR TYR PRO ASP THR VAL LYS SEQRES 6 H 216 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN SER SEQRES 7 H 216 HIS TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 H 216 ALA VAL TYR PHE CYS ALA SER PRO TYR GLY GLY TYR PHE SEQRES 9 H 216 ASP VAL TRP GLY GLN GLY THR LEU VAL THR VAL SER SER SEQRES 10 H 216 ALA SER THR LYS GLY PRO SER VAL PHE PRO LEU ALA PRO SEQRES 11 H 216 CYS SER ARG SER THR SER GLU SER THR ALA ALA LEU GLY SEQRES 12 H 216 CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL THR VAL SEQRES 13 H 216 SER TRP ASN SER GLY ALA LEU THR SER GLY VAL HIS THR SEQRES 14 H 216 PHE PRO ALA VAL LEU GLN SER SER GLY LEU TYR SER LEU SEQRES 15 H 216 SER SER VAL VAL THR VAL PRO SER SER SER LEU GLY THR SEQRES 16 H 216 LYS THR TYR THR CYS ASN VAL ASP HIS LYS PRO SER ASN SEQRES 17 H 216 THR LYS VAL ASP LYS ARG VAL GLU SEQRES 1 L 214 GLU ILE VAL LEU THR GLN SER PRO ALA THR LEU SER LEU SEQRES 2 L 214 SER PRO GLY GLU ARG ALA THR LEU SER CYS ARG ALA SER SEQRES 3 L 214 GLN SER ILE SER ASN PHE LEU HIS TRP TYR GLN GLN LYS SEQRES 4 L 214 PRO GLY GLN ALA PRO ARG LEU LEU ILE LYS TYR ALA SER SEQRES 5 L 214 GLN SER ILE SER GLY ILE PRO ALA ARG PHE SER GLY SER SEQRES 6 L 214 GLY SER GLY THR ASP PHE THR LEU THR ILE SER SER LEU SEQRES 7 L 214 GLU PRO GLU ASP PHE ALA VAL TYR PHE CYS GLN GLN SER SEQRES 8 L 214 ASN SER TRP PRO HIS THR PHE GLY GLN GLY THR LYS VAL SEQRES 9 L 214 GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE SEQRES 10 L 214 PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SEQRES 11 L 214 SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU SEQRES 12 L 214 ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER SEQRES 13 L 214 GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS SEQRES 14 L 214 ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SER SEQRES 15 L 214 LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU SEQRES 16 L 214 VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER SEQRES 17 L 214 PHE ASN ARG GLY GLU CYS HET THR A 201 8 HET GOL A 202 6 HET GOL A 203 12 HET EDO A 204 4 HET MG H 301 1 HET GOL H 302 6 HET GOL H 303 6 HET EDO H 304 4 HET EDO H 305 4 HET EDO H 306 4 HET EDO H 307 4 HET GOL L 301 6 HET PEG L 302 7 HET EDO L 303 4 HET EDO L 304 4 HET GOL L 305 6 HET GOL L 306 6 HET MG L 307 1 HET CL L 308 1 HETNAM THR THREONINE HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETNAM MG MAGNESIUM ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 4 THR C4 H9 N O3 FORMUL 5 GOL 7(C3 H8 O3) FORMUL 7 EDO 7(C2 H6 O2) FORMUL 8 MG 2(MG 2+) FORMUL 16 PEG C4 H10 O3 FORMUL 22 CL CL 1- FORMUL 23 HOH *789(H2 O) HELIX 1 AA1 ARG A 114 SER A 118 5 5 HELIX 2 AA2 ALA H 28 TYR H 32 5 5 HELIX 3 AA3 ASN H 74 LYS H 76 5 3 HELIX 4 AA4 ARG H 87 THR H 91 5 5 HELIX 5 AA5 SER H 160 ALA H 162 5 3 HELIX 6 AA6 SER H 191 GLY H 194 5 4 HELIX 7 AA7 LYS H 205 ASN H 208 5 4 HELIX 8 AA8 GLU L 79 PHE L 83 5 5 HELIX 9 AA9 GLU L 123 SER L 127 5 5 HELIX 10 AB1 LYS L 183 GLU L 187 1 5 SHEET 1 AA1 4 THR A 36 SER A 38 0 SHEET 2 AA1 4 ALA A 50 SER A 55 -1 O THR A 53 N SER A 38 SHEET 3 AA1 4 ASP A 105 VAL A 110 -1 O MET A 108 N PHE A 52 SHEET 4 AA1 4 PHE A 95 GLN A 99 -1 N ARG A 96 O SER A 109 SHEET 1 AA2 5 LEU A 41 THR A 45 0 SHEET 2 AA2 5 ALA A 140 THR A 145 1 O ARG A 143 N LEU A 42 SHEET 3 AA2 5 GLY A 119 SER A 127 -1 N GLY A 119 O LEU A 142 SHEET 4 AA2 5 PHE A 63 MET A 70 -1 N ASN A 66 O GLY A 124 SHEET 5 AA2 5 THR A 76 PHE A 82 -1 O LEU A 79 N TRP A 67 SHEET 1 AA3 4 LEU A 41 THR A 45 0 SHEET 2 AA3 4 ALA A 140 THR A 145 1 O ARG A 143 N LEU A 42 SHEET 3 AA3 4 GLY A 119 SER A 127 -1 N GLY A 119 O LEU A 142 SHEET 4 AA3 4 GLN A 133 GLU A 136 -1 O LYS A 135 N ALA A 125 SHEET 1 AA4 4 LYS H 3 SER H 7 0 SHEET 2 AA4 4 LEU H 18 SER H 25 -1 O ALA H 23 N VAL H 5 SHEET 3 AA4 4 SER H 78 MET H 83 -1 O MET H 83 N LEU H 18 SHEET 4 AA4 4 PHE H 68 ASP H 73 -1 N ASP H 73 O SER H 78 SHEET 1 AA5 6 LEU H 11 VAL H 12 0 SHEET 2 AA5 6 THR H 111 VAL H 115 1 O THR H 114 N VAL H 12 SHEET 3 AA5 6 ALA H 92 TYR H 100 -1 N TYR H 94 O THR H 111 SHEET 4 AA5 6 MET H 34 GLN H 39 -1 N VAL H 37 O PHE H 95 SHEET 5 AA5 6 GLU H 46 ILE H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 AA5 6 THR H 58 TYR H 59 -1 O TYR H 59 N THR H 50 SHEET 1 AA6 4 LEU H 11 VAL H 12 0 SHEET 2 AA6 4 THR H 111 VAL H 115 1 O THR H 114 N VAL H 12 SHEET 3 AA6 4 ALA H 92 TYR H 100 -1 N TYR H 94 O THR H 111 SHEET 4 AA6 4 TYR H 103 TRP H 107 -1 O TYR H 103 N TYR H 100 SHEET 1 AA7 4 SER H 124 LEU H 128 0 SHEET 2 AA7 4 THR H 139 TYR H 149 -1 O LYS H 147 N SER H 124 SHEET 3 AA7 4 TYR H 180 PRO H 189 -1 O LEU H 182 N VAL H 146 SHEET 4 AA7 4 VAL H 167 THR H 169 -1 N HIS H 168 O VAL H 185 SHEET 1 AA8 4 SER H 124 LEU H 128 0 SHEET 2 AA8 4 THR H 139 TYR H 149 -1 O LYS H 147 N SER H 124 SHEET 3 AA8 4 TYR H 180 PRO H 189 -1 O LEU H 182 N VAL H 146 SHEET 4 AA8 4 VAL H 173 LEU H 174 -1 N VAL H 173 O SER H 181 SHEET 1 AA9 3 THR H 155 TRP H 158 0 SHEET 2 AA9 3 THR H 199 HIS H 204 -1 O ASN H 201 N SER H 157 SHEET 3 AA9 3 THR H 209 ARG H 214 -1 O VAL H 211 N VAL H 202 SHEET 1 AB1 4 LEU L 4 SER L 7 0 SHEET 2 AB1 4 ALA L 19 ALA L 25 -1 O ARG L 24 N THR L 5 SHEET 3 AB1 4 ASP L 70 ILE L 75 -1 O LEU L 73 N LEU L 21 SHEET 4 AB1 4 PHE L 62 SER L 67 -1 N SER L 63 O THR L 74 SHEET 1 AB2 6 THR L 10 LEU L 13 0 SHEET 2 AB2 6 THR L 102 ILE L 106 1 O GLU L 105 N LEU L 11 SHEET 3 AB2 6 ALA L 84 GLN L 90 -1 N ALA L 84 O VAL L 104 SHEET 4 AB2 6 LEU L 33 GLN L 38 -1 N GLN L 38 O VAL L 85 SHEET 5 AB2 6 ARG L 45 LYS L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 AB2 6 GLN L 53 SER L 54 -1 O GLN L 53 N LYS L 49 SHEET 1 AB3 4 THR L 10 LEU L 13 0 SHEET 2 AB3 4 THR L 102 ILE L 106 1 O GLU L 105 N LEU L 11 SHEET 3 AB3 4 ALA L 84 GLN L 90 -1 N ALA L 84 O VAL L 104 SHEET 4 AB3 4 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 AB4 4 SER L 114 PHE L 118 0 SHEET 2 AB4 4 THR L 129 PHE L 139 -1 O LEU L 135 N PHE L 116 SHEET 3 AB4 4 TYR L 173 SER L 182 -1 O LEU L 179 N VAL L 132 SHEET 4 AB4 4 SER L 159 VAL L 163 -1 N GLN L 160 O THR L 178 SHEET 1 AB5 4 ALA L 153 LEU L 154 0 SHEET 2 AB5 4 LYS L 145 VAL L 150 -1 N VAL L 150 O ALA L 153 SHEET 3 AB5 4 VAL L 191 THR L 197 -1 O GLU L 195 N GLN L 147 SHEET 4 AB5 4 VAL L 205 ASN L 210 -1 O LYS L 207 N CYS L 194 SSBOND 1 CYS A 54 CYS A 123 1555 1555 2.18 SSBOND 2 CYS H 22 CYS H 96 1555 1555 2.14 SSBOND 3 CYS H 144 CYS H 200 1555 1555 2.02 SSBOND 4 CYS L 23 CYS L 88 1555 1555 2.20 SSBOND 5 CYS L 134 CYS L 194 1555 1555 1.96 LINK O HOH A 464 MG MG H 301 1555 1555 2.47 LINK O ASP H 105 MG MG H 301 1555 1555 2.81 LINK MG MG H 301 O HOH L 587 1555 1555 2.52 LINK O1 EDO H 307 MG MG L 307 1555 1555 2.63 LINK O GLN L 160 MG MG L 307 1555 1555 2.85 LINK O BSER L 176 MG MG L 307 1555 1555 2.60 LINK OG ASER L 176 MG MG L 307 1555 1555 2.76 LINK OG1 THR L 178 MG MG L 307 1555 1555 2.99 CISPEP 1 SER A 38 PRO A 39 0 -6.47 CISPEP 2 PHE A 82 PRO A 83 0 -12.63 CISPEP 3 ALA A 129 PRO A 130 0 -0.58 CISPEP 4 PHE H 150 PRO H 151 0 -5.35 CISPEP 5 GLU H 152 PRO H 153 0 -10.28 CISPEP 6 GLU H 152 PRO H 153 0 -8.12 CISPEP 7 SER L 7 PRO L 8 0 -8.22 CISPEP 8 TRP L 94 PRO L 95 0 -1.13 CISPEP 9 TRP L 94 PRO L 95 0 -5.75 CISPEP 10 TYR L 140 PRO L 141 0 0.37 CRYST1 56.290 68.410 77.310 90.00 99.44 90.00 P 1 21 1 2 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 0.017765 0.000000 0.002954 0.00000 SCALE2 0.000000 0.014618 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013113 0.00000