HEADER HYDROLASE 14-JAN-10 3LE7 TITLE CRYSTAL STRUCTURE OF PD-L1 FROM P. DIOICA IN COMPLEX WITH ADENINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOME-INACTIVATING PROTEIN PD-L1/PD-L2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RRNA N-GLYCOSIDASE PD-L1/PD-L2; COMPND 5 EC: 3.2.2.22 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHYTOLACCA DIOICA; SOURCE 3 ORGANISM_COMMON: BELLA SOMBRA TREE; SOURCE 4 ORGANISM_TAXID: 29725 KEYWDS RIBOSOME, ADENINE, DISULFIDE BOND, GLYCOPROTEIN, HYDROLASE, PLANT KEYWDS 2 DEFENSE, PROTEIN SYNTHESIS INHIBITOR, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR A.RUGGIERO,R.BERISIO REVDAT 3 01-NOV-23 3LE7 1 HETSYN REVDAT 2 29-JUL-20 3LE7 1 COMPND REMARK HETNAM LINK REVDAT 2 2 1 SITE REVDAT 1 14-APR-10 3LE7 0 JRNL AUTH V.SEVERINO,A.CHAMBERY,A.DI MARO,D.MARASCO,A.RUGGIERO, JRNL AUTH 2 R.BERISIO,F.GIANSANTI,R.IPPOLITI,A.PARENTE JRNL TITL THE ROLE OF THE GLYCAN MOIETY ON THE STRUCTURE-FUNCTION JRNL TITL 2 RELATIONSHIPS OF PD-L1, TYPE 1 RIBOSOME-INACTIVATING PROTEIN JRNL TITL 3 FROM P. DIOICA LEAVES JRNL REF MOL BIOSYST V. 6 570 2010 JRNL REFN ISSN 1742-206X JRNL PMID 20174685 JRNL DOI 10.1039/B919801F 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) : 9.97 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 84.9 REMARK 3 NUMBER OF REFLECTIONS : 41131 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) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2167 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) : 2740 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.28 REMARK 3 BIN R VALUE (WORKING SET) : 0.2590 REMARK 3 BIN FREE R VALUE SET COUNT : 147 REMARK 3 BIN FREE R VALUE : 0.3500 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4100 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 62 REMARK 3 SOLVENT ATOMS : 659 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.04000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.05000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.154 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.094 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.173 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.923 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.898 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4289 ; 0.037 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5811 ; 2.604 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 522 ; 6.990 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 196 ;36.214 ;25.510 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 783 ;13.841 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;25.509 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 672 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3165 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 6148 ; 0.303 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3466 ; 0.383 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 1462 ; 0.264 ; 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): 323 ; 0.297 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 136 ; 0.264 ; 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): 2618 ; 0.957 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4257 ; 1.633 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1800 ; 2.134 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1554 ; 3.397 ; 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 : 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: NULL REMARK 4 REMARK 4 3LE7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-FEB-10. REMARK 100 THE DEPOSITION ID IS D_1000057167. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUL-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R 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 : NI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56763 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.7000 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) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.07000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: IL MILIONE REMARK 200 STARTING MODEL: 3H5K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.16M SODIUM ACETATE TRIHYDRATE, 0.1M REMARK 280 SODIUM CACODYLATE, 24% PEG8000, 3MM ADENINE, PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 74.66150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.07950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 74.66150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 16.07950 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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: 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 O6 NAG A 265 O HOH A 524 2.06 REMARK 500 O HOH A 468 O HOH A 524 2.07 REMARK 500 O HOH B 334 O HOH B 599 2.07 REMARK 500 O HOH B 353 O HOH B 657 2.09 REMARK 500 O HOH B 372 O HOH B 540 2.10 REMARK 500 OD1 ASP A 201 O HOH A 640 2.11 REMARK 500 OD2 ASP B 115 O HOH B 275 2.12 REMARK 500 OE2 GLU B 24 O HOH B 649 2.13 REMARK 500 CE1 TYR B 121 O HOH B 644 2.13 REMARK 500 O LYS B 227 O HOH B 589 2.13 REMARK 500 CG ASN A 13 C1 NAG A 3 2.14 REMARK 500 OG1 THR A 260 O HOH A 648 2.14 REMARK 500 O ASN A 45 O HOH A 624 2.14 REMARK 500 ND2 ASN B 13 C2 NAG B 2 2.15 REMARK 500 OD1 ASN B 122 OG1 THR B 127 2.15 REMARK 500 OD1 ASN A 45 O HOH A 627 2.15 REMARK 500 O ASP A 32 O HOH A 382 2.16 REMARK 500 OG SER A 48 O HOH A 624 2.16 REMARK 500 O HOH A 584 O HOH A 659 2.17 REMARK 500 OD1 ASP A 81 NE2 HIS A 90 2.17 REMARK 500 O HOH A 403 O HOH A 661 2.17 REMARK 500 OG SER A 159 O HOH A 528 2.18 REMARK 500 NE2 GLN A 62 O HOH A 285 2.18 REMARK 500 O LEU B 67 O HOH B 656 2.18 REMARK 500 OD1 ASP B 205 O HOH B 410 2.19 REMARK 500 O LEU A 35 O HOH A 382 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 ND2 ASN A 28 NZ LYS A 238 1545 2.06 REMARK 500 ND2 ASN B 17 O ASP B 235 1565 2.06 REMARK 500 OE2 GLU A 104 OG SER B 111 3445 2.10 REMARK 500 O HOH A 432 O HOH B 483 1565 2.13 REMARK 500 O HOH B 390 O HOH B 508 1545 2.19 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 CYS A 37 CB CYS A 37 SG -0.097 REMARK 500 CYS A 87 CB CYS A 87 SG -0.111 REMARK 500 TYR A 184 CD1 TYR A 184 CE1 -0.108 REMARK 500 GLU A 207 CG GLU A 207 CD -0.091 REMARK 500 TRP A 210 CB TRP A 210 CG -0.131 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 27 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG B 27 NE - CZ - NH2 ANGL. DEV. = -4.7 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 GLN A 36 138.41 -171.00 REMARK 500 ASN A 45 -178.74 -64.42 REMARK 500 ASN A 120 46.70 -73.26 REMARK 500 TYR A 121 155.53 179.64 REMARK 500 ASN B 45 -175.63 -64.88 REMARK 500 CYS B 108 45.32 -109.34 REMARK 500 SER B 110 43.10 -72.03 REMARK 500 SER B 111 -16.07 -34.50 REMARK 500 SER B 112 -39.22 -35.72 REMARK 500 ASN B 120 46.99 -70.36 REMARK 500 TYR B 121 162.35 177.45 REMARK 500 VAL B 176 -71.01 -110.53 REMARK 500 LEU B 231 -168.73 -111.12 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 ILE A 95 THR A 96 -148.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 NAG A 265 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3H5K RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PD-L1 FROM P. DIOICA DBREF 3LE7 A 4 264 UNP P84853 RIPL1_PHYDI 1 261 DBREF 3LE7 B 4 264 UNP P84853 RIPL1_PHYDI 1 261 SEQRES 1 A 261 ILE ASN THR ILE THR TYR ASP ALA GLY ASN THR THR ILE SEQRES 2 A 261 ASN LYS TYR ALA THR PHE MET GLU SER LEU ARG ASN GLU SEQRES 3 A 261 ALA LYS ASP PRO SER LEU GLN CYS TYR GLY ILE PRO MET SEQRES 4 A 261 LEU PRO ASN ASN SER SER THR ILE LYS TYR LEU LEU VAL SEQRES 5 A 261 LYS LEU GLN GLY ALA SER GLN LYS THR ILE THR LEU MET SEQRES 6 A 261 LEU ARG ARG ASN ASN LEU TYR VAL MET GLY TYR SER ASP SEQRES 7 A 261 PRO PHE ASN GLY ASN CYS ARG TYR HIS ILE PHE ASN ASP SEQRES 8 A 261 ILE THR GLY THR GLU ARG THR ASN VAL GLU ASN THR LEU SEQRES 9 A 261 CYS SER SER SER SER SER ARG ASP ALA LYS PRO ILE ASN SEQRES 10 A 261 TYR ASN SER LEU TYR SER THR LEU GLU LYS LYS ALA GLU SEQRES 11 A 261 VAL ASN SER ARG SER GLN VAL GLN LEU GLY ILE GLN ILE SEQRES 12 A 261 LEU SER SER ASP ILE GLY LYS ILE SER GLY GLN SER SER SEQRES 13 A 261 PHE THR ASP LYS THR GLU ALA LYS PHE LEU LEU VAL ALA SEQRES 14 A 261 ILE GLN MET VAL SER GLU ALA ALA ARG PHE LYS TYR ILE SEQRES 15 A 261 GLU ASN GLN VAL LYS THR ASN PHE ASN ARG ASP PHE SER SEQRES 16 A 261 PRO ASN ASP LYS ILE LEU ASP LEU GLU GLU ASN TRP GLY SEQRES 17 A 261 LYS ILE SER THR ALA ILE HIS ASP ALA THR ASN GLY ALA SEQRES 18 A 261 LEU PRO LYS PRO LEU GLU LEU LYS ASN ALA ASP GLY THR SEQRES 19 A 261 LYS TRP ILE VAL LEU ARG VAL ASP GLU ILE LYS PRO ASP SEQRES 20 A 261 MET GLY LEU LEU ASN TYR VAL ASN GLY THR CYS GLN THR SEQRES 21 A 261 THR SEQRES 1 B 261 ILE ASN THR ILE THR TYR ASP ALA GLY ASN THR THR ILE SEQRES 2 B 261 ASN LYS TYR ALA THR PHE MET GLU SER LEU ARG ASN GLU SEQRES 3 B 261 ALA LYS ASP PRO SER LEU GLN CYS TYR GLY ILE PRO MET SEQRES 4 B 261 LEU PRO ASN ASN SER SER THR ILE LYS TYR LEU LEU VAL SEQRES 5 B 261 LYS LEU GLN GLY ALA SER GLN LYS THR ILE THR LEU MET SEQRES 6 B 261 LEU ARG ARG ASN ASN LEU TYR VAL MET GLY TYR SER ASP SEQRES 7 B 261 PRO PHE ASN GLY ASN CYS ARG TYR HIS ILE PHE ASN ASP SEQRES 8 B 261 ILE THR GLY THR GLU ARG THR ASN VAL GLU ASN THR LEU SEQRES 9 B 261 CYS SER SER SER SER SER ARG ASP ALA LYS PRO ILE ASN SEQRES 10 B 261 TYR ASN SER LEU TYR SER THR LEU GLU LYS LYS ALA GLU SEQRES 11 B 261 VAL ASN SER ARG SER GLN VAL GLN LEU GLY ILE GLN ILE SEQRES 12 B 261 LEU SER SER ASP ILE GLY LYS ILE SER GLY GLN SER SER SEQRES 13 B 261 PHE THR ASP LYS THR GLU ALA LYS PHE LEU LEU VAL ALA SEQRES 14 B 261 ILE GLN MET VAL SER GLU ALA ALA ARG PHE LYS TYR ILE SEQRES 15 B 261 GLU ASN GLN VAL LYS THR ASN PHE ASN ARG ASP PHE SER SEQRES 16 B 261 PRO ASN ASP LYS ILE LEU ASP LEU GLU GLU ASN TRP GLY SEQRES 17 B 261 LYS ILE SER THR ALA ILE HIS ASP ALA THR ASN GLY ALA SEQRES 18 B 261 LEU PRO LYS PRO LEU GLU LEU LYS ASN ALA ASP GLY THR SEQRES 19 B 261 LYS TRP ILE VAL LEU ARG VAL ASP GLU ILE LYS PRO ASP SEQRES 20 B 261 MET GLY LEU LEU ASN TYR VAL ASN GLY THR CYS GLN THR SEQRES 21 B 261 THR MODRES 3LE7 ASN B 13 ASN GLYCOSYLATION SITE MODRES 3LE7 ASN A 13 ASN GLYCOSYLATION SITE HET NAG A 3 14 HET NAG A 265 14 HET ADE A 501 10 HET NAG B 2 14 HET ADE B 601 10 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM ADE ADENINE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 3 NAG 3(C8 H15 N O6) FORMUL 5 ADE 2(C5 H5 N5) FORMUL 8 HOH *659(H2 O) HELIX 1 1 THR A 15 LYS A 31 1 17 HELIX 2 2 ALA A 60 GLN A 62 5 3 HELIX 3 3 GLY A 97 CYS A 108 1 12 HELIX 4 4 LEU A 124 ALA A 132 1 9 HELIX 5 5 SER A 136 VAL A 140 5 5 HELIX 6 6 GLY A 143 SER A 155 1 13 HELIX 7 7 THR A 161 PHE A 182 1 22 HELIX 8 8 PHE A 182 ASN A 192 1 11 HELIX 9 9 ASN A 200 ASP A 219 1 20 HELIX 10 10 VAL A 244 LYS A 248 1 5 HELIX 11 11 PRO A 249 MET A 251 5 3 HELIX 12 12 THR B 15 LYS B 31 1 17 HELIX 13 13 ALA B 60 GLN B 62 5 3 HELIX 14 14 THR B 96 CYS B 108 1 13 HELIX 15 15 LEU B 124 ALA B 132 1 9 HELIX 16 16 SER B 136 VAL B 140 5 5 HELIX 17 17 GLY B 143 SER B 155 1 13 HELIX 18 18 THR B 161 VAL B 176 1 16 HELIX 19 19 VAL B 176 PHE B 182 1 7 HELIX 20 20 PHE B 182 ASN B 192 1 11 HELIX 21 21 ASN B 200 ALA B 220 1 21 HELIX 22 22 VAL B 244 LYS B 248 1 5 HELIX 23 23 PRO B 249 MET B 251 5 3 SHEET 1 A 6 ASN A 5 ASP A 10 0 SHEET 2 A 6 TYR A 52 GLN A 58 1 O LYS A 56 N TYR A 9 SHEET 3 A 6 THR A 64 ARG A 70 -1 O LEU A 67 N VAL A 55 SHEET 4 A 6 VAL A 76 PHE A 83 -1 O MET A 77 N MET A 68 SHEET 5 A 6 ASN A 86 ILE A 91 -1 O HIS A 90 N TYR A 79 SHEET 6 A 6 ARG A 114 ALA A 116 1 O ASP A 115 N CYS A 87 SHEET 1 B 2 GLN A 36 CYS A 37 0 SHEET 2 B 2 ILE A 40 PRO A 41 -1 O ILE A 40 N CYS A 37 SHEET 1 C 2 ALA A 224 LYS A 232 0 SHEET 2 C 2 LYS A 238 ARG A 243 -1 O TRP A 239 N LEU A 231 SHEET 1 D 6 ASN B 5 ASP B 10 0 SHEET 2 D 6 TYR B 52 GLN B 58 1 O LYS B 56 N TYR B 9 SHEET 3 D 6 THR B 64 ARG B 70 -1 O LEU B 67 N VAL B 55 SHEET 4 D 6 VAL B 76 PHE B 83 -1 O MET B 77 N MET B 68 SHEET 5 D 6 ASN B 86 ILE B 91 -1 O HIS B 90 N TYR B 79 SHEET 6 D 6 ARG B 114 ALA B 116 1 O ASP B 115 N TYR B 89 SHEET 1 E 2 GLN B 36 CYS B 37 0 SHEET 2 E 2 ILE B 40 PRO B 41 -1 O ILE B 40 N CYS B 37 SHEET 1 F 2 ALA B 224 LYS B 232 0 SHEET 2 F 2 LYS B 238 ARG B 243 -1 O TRP B 239 N LEU B 231 SSBOND 1 CYS A 37 CYS A 261 1555 1555 2.02 SSBOND 2 CYS A 87 CYS A 108 1555 1555 1.99 SSBOND 3 CYS B 37 CYS B 261 1555 1555 1.99 SSBOND 4 CYS B 87 CYS B 108 1555 1555 2.00 LINK C1 NAG A 3 ND2 ASN A 13 1555 1555 1.43 LINK C1 NAG B 2 ND2 ASN B 13 1555 1555 1.43 CRYST1 149.323 32.159 112.295 90.00 128.29 90.00 C 1 2 1 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 0.006697 0.000000 0.005286 0.00000 SCALE2 0.000000 0.031095 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011345 0.00000