HEADER ANTITUMOR PROTEIN 20-JUL-21 7RJF TITLE MOPD-1 MUTANT-L47W COMPND MOL_ID: 1; COMPND 2 MOLECULE: [L47W]MOPD-1; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS SYNTHETIC PEPTIDE, DISULFIDE-RICH PEPTIDE, ANTITUMOR PEPTIDE, PEPTIDE KEYWDS 2 MIMETIC, ANTITUMOR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.HUAWU,K.W.CONAN,J.K.GORDON,M.C.BRETT,H.YEN-HUA,J.C.DAVID REVDAT 3 18-OCT-23 7RJF 1 REMARK REVDAT 2 24-NOV-21 7RJF 1 JRNL REVDAT 1 27-OCT-21 7RJF 0 JRNL AUTH H.YIN,X.ZHOU,Y.H.HUANG,G.J.KING,B.M.COLLINS,Y.GAO,D.J.CRAIK, JRNL AUTH 2 C.K.WANG JRNL TITL RATIONAL DESIGN OF POTENT PEPTIDE INHIBITORS OF THE JRNL TITL 2 PD-1:PD-L1 INTERACTION FOR CANCER IMMUNOTHERAPY. JRNL REF J.AM.CHEM.SOC. V. 143 18536 2021 JRNL REFN ESSN 1520-5126 JRNL PMID 34661406 JRNL DOI 10.1021/JACS.1C08132 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 10899 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1091 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 39.3500 - 3.6000 1.00 1365 152 0.2038 0.2482 REMARK 3 2 3.6000 - 2.8600 1.00 1256 140 0.2367 0.3119 REMARK 3 3 2.8600 - 2.5000 1.00 1230 136 0.2463 0.3072 REMARK 3 4 2.4900 - 2.2700 1.00 1220 136 0.2563 0.2697 REMARK 3 5 2.2700 - 2.1000 1.00 1205 134 0.2560 0.2856 REMARK 3 6 2.1000 - 1.9800 1.00 1203 133 0.2555 0.2370 REMARK 3 7 1.9800 - 1.8800 1.00 1181 132 0.2646 0.2946 REMARK 3 8 1.8800 - 1.8000 0.95 1148 128 0.3103 0.3416 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.204 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.643 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.012 826 REMARK 3 ANGLE : 1.134 1096 REMARK 3 CHIRALITY : 0.076 102 REMARK 3 PLANARITY : 0.007 148 REMARK 3 DIHEDRAL : 32.632 330 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7RJF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1000258280. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10906 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 42.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.5500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.23100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PDB ENTRY 5JG9 (SCAFFOLD) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 NL 5 MG/ML PEPTIDE + 200 NL 0.1 M REMARK 280 ZINC CHLORIDE, 8% V/V TACSIMATE, PH 6.0, 16% W/V PEG3350, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293.15K 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 63.69950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 20.68850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 20.68850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 31.84975 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 20.68850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 20.68850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 95.54925 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 20.68850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 20.68850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 31.84975 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 20.68850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 20.68850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 95.54925 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 63.69950 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 CYS A 29 -159.41 -116.47 REMARK 500 REMARK 500 REMARK: NULL 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 ZN A 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 22 OE1 REMARK 620 2 GLU A 25 OE1 99.4 REMARK 620 3 HIS A 34 ND1 52.3 76.1 REMARK 620 4 HIS B 30 NE2 59.9 76.3 8.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 30 NE2 REMARK 620 2 MLI A 103 O8 110.0 REMARK 620 3 MLI A 104 O8 126.7 74.8 REMARK 620 4 MLI A 104 O9 93.3 127.1 53.8 REMARK 620 5 HIS B 34 ND1 116.0 115.7 107.2 92.9 REMARK 620 N 1 2 3 4 DBREF 7RJF A 1 47 PDB 7RJF 7RJF 1 47 DBREF 7RJF B 1 47 PDB 7RJF 7RJF 1 47 SEQRES 1 A 47 ILE GLN ILE ARG GLU TYR LYS ARG CYS GLY GLN ASP GLU SEQRES 2 A 47 GLU ARG VAL ARG ARG GLU CYS LYS GLU ARG GLY GLU ARG SEQRES 3 A 47 GLN ASN CYS HIS TYR VAL ILE HIS LYS GLU GLY ASN CYS SEQRES 4 A 47 TYR VAL CYS GLY ILE ILE CYS TRP SEQRES 1 B 47 ILE GLN ILE ARG GLU TYR LYS ARG CYS GLY GLN ASP GLU SEQRES 2 B 47 GLU ARG VAL ARG ARG GLU CYS LYS GLU ARG GLY GLU ARG SEQRES 3 B 47 GLN ASN CYS HIS TYR VAL ILE HIS LYS GLU GLY ASN CYS SEQRES 4 B 47 TYR VAL CYS GLY ILE ILE CYS TRP HET ZN A 101 1 HET ZN A 102 1 HET MLI A 103 9 HET MLI A 104 9 HETNAM ZN ZINC ION HETNAM MLI MALONATE ION FORMUL 3 ZN 2(ZN 2+) FORMUL 5 MLI 2(C3 H2 O4 2-) FORMUL 7 HOH *25(H2 O) HELIX 1 AA1 ASP A 12 ASN A 28 1 17 HELIX 2 AA2 ASP B 12 ASN B 28 1 17 SHEET 1 AA1 3 GLN A 2 CYS A 9 0 SHEET 2 AA1 3 CYS A 39 CYS A 46 -1 O CYS A 42 N TYR A 6 SHEET 3 AA1 3 HIS A 30 GLU A 36 -1 N GLU A 36 O CYS A 39 SHEET 1 AA2 3 GLN B 2 ARG B 8 0 SHEET 2 AA2 3 CYS B 39 CYS B 46 -1 O CYS B 42 N TYR B 6 SHEET 3 AA2 3 HIS B 30 GLU B 36 -1 N GLU B 36 O CYS B 39 SSBOND 1 CYS A 9 CYS A 39 1555 1555 2.01 SSBOND 2 CYS A 20 CYS A 42 1555 1555 2.04 SSBOND 3 CYS A 29 CYS A 46 1555 1555 2.03 SSBOND 4 CYS B 9 CYS B 39 1555 1555 2.04 SSBOND 5 CYS B 20 CYS B 42 1555 1555 2.05 SSBOND 6 CYS B 29 CYS B 46 1555 1555 2.06 LINK OE1 GLU A 22 ZN ZN A 101 1555 6465 2.02 LINK OE1 GLU A 25 ZN ZN A 101 1555 6465 1.93 LINK NE2 HIS A 30 ZN ZN A 102 1555 1555 2.11 LINK ND1 HIS A 34 ZN ZN A 101 1555 1555 2.12 LINK ZN ZN A 101 NE2 HIS B 30 1555 1555 2.08 LINK ZN ZN A 102 O8 MLI A 103 1555 1555 2.06 LINK ZN ZN A 102 O8 MLI A 104 1555 1555 1.94 LINK ZN ZN A 102 O9 MLI A 104 1555 1555 2.66 LINK ZN ZN A 102 ND1 HIS B 34 1555 1555 2.16 CRYST1 41.377 41.377 127.399 90.00 90.00 90.00 P 41 21 2 16 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 0.024168 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024168 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007849 0.00000