HEADER IMMUNE SYSTEM 31-MAR-17 5VCL TITLE STRUCTURE OF THE QDM PEPTIDE BOUND TO QA-1A COMPND MOL_ID: 1; COMPND 2 MOLECULE: H2-T23 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 21-297; COMPND 5 SYNONYM: MHC QA-1A,QA-1; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: ECTODOMAIN RESIDUES 21-297; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: BETA-2-MICROGLOBULIN; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: UNP RESIDUES 21-119; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: QDM PEPTIDE; COMPND 15 CHAIN: P; COMPND 16 FRAGMENT: UNP RESIDUES 3-11; COMPND 17 SYNONYM: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, L-D ALPHA CHAIN; COMPND 18 ENGINEERED: YES; COMPND 19 OTHER_DETAILS: PEPTIDE FROM MHC-CLASS IA LEADER SEQUENCE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: H2-T23; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET22B+; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 12 ORGANISM_COMMON: MOUSE; SOURCE 13 ORGANISM_TAXID: 10090; SOURCE 14 GENE: B2M; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PET22B+; SOURCE 19 MOL_ID: 3; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 22 ORGANISM_COMMON: MOUSE; SOURCE 23 ORGANISM_TAXID: 10090 KEYWDS ANTIGEN-PRESENTATION, IMMUNE SYSTEM, MHC EXPDTA X-RAY DIFFRACTION AUTHOR G.YING,D.M.ZAJONC REVDAT 2 04-OCT-23 5VCL 1 LINK REVDAT 1 25-OCT-17 5VCL 0 JRNL AUTH G.YING,J.WANG,V.KUMAR,D.M.ZAJONC JRNL TITL CRYSTAL STRUCTURE OF QA-1A WITH BOUND QA-1 DETERMINANT JRNL TITL 2 MODIFIER PEPTIDE. JRNL REF PLOS ONE V. 12 82296 2017 JRNL REFN ESSN 1932-6203 JRNL PMID 28767728 JRNL DOI 10.1371/JOURNAL.PONE.0182296 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 32899 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) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1073 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2152 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.3650 REMARK 3 BIN FREE R VALUE SET COUNT : 72 REMARK 3 BIN FREE R VALUE : 0.4060 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3159 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : 0.00000 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): 0.186 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.162 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.144 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.753 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3278 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2877 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4447 ; 1.305 ; 1.941 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6700 ; 0.904 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 382 ; 6.410 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 167 ;33.794 ;23.533 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 535 ;13.086 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;14.496 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 455 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3612 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 696 ; 0.001 ; 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): 1537 ; 1.873 ; 3.677 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1536 ; 1.873 ; 3.677 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1916 ; 3.056 ; 5.500 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1917 ; 3.055 ; 5.499 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1741 ; 2.075 ; 3.915 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1741 ; 2.075 ; 3.915 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2532 ; 3.413 ; 5.777 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3541 ; 5.318 ;40.907 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3542 ; 5.317 ;40.920 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 : NULL 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 5VCL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-APR-17. REMARK 100 THE DEPOSITION ID IS D_1000227227. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-FEB-16 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 : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.12 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34634 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 41.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.59600 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: 3VJ6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5% POLYETHYLENE GLYCOL 1000, 40% REMARK 280 ETHYLENE GLYCOL, 100 MM HEPES PH 6.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 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,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 33.60350 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.60550 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 33.60350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 52.60550 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: 6210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -92.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, P 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 459 LIES ON A SPECIAL POSITION. 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 MET A 0 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 GLU A 91 CG CD OE1 OE2 REMARK 470 GLU A 196 CG CD OE1 OE2 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 ASP A 29 -125.21 50.97 REMARK 500 THR A 136 -52.04 -124.56 REMARK 500 ASP A 151 55.88 38.24 REMARK 500 SER A 195 44.95 -163.75 REMARK 500 GLU A 196 -45.65 65.65 REMARK 500 LEU A 224 59.68 -92.19 REMARK 500 LYS B 48 68.62 64.34 REMARK 500 ASP B 53 132.05 19.79 REMARK 500 TRP B 60 -3.03 75.52 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 NA A 305 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 10 OG1 REMARK 620 2 MET B 54 O 113.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 304 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 29 OD2 REMARK 620 2 LEU A 179 O 127.5 REMARK 620 3 TYR A 209 OH 121.3 110.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 309 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 38 OG REMARK 620 2 ASP A 39 OD1 103.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 306 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 77 OD1 REMARK 620 2 GLU A 116 OE2 139.4 REMARK 620 3 THR P 6 OG1 128.4 86.2 REMARK 620 4 LEU P 7 O 62.0 107.6 85.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VJ6 RELATED DB: PDB REMARK 900 3VJ6 (QA-1B) IS AN ALLOTYPE OF QA-1A AND BINDS THE SAME PEPTIDE QDM. DBREF 5VCL A 1 277 UNP Q31153 Q31153_MOUSE 21 297 DBREF 5VCL B 1 99 UNP P01887 B2MG_MOUSE 21 119 DBREF 5VCL P 1 9 UNP P01897 HA1L_MOUSE 3 11 SEQADV 5VCL MET A 0 UNP Q31153 INITIATING METHIONINE SEQRES 1 A 278 MET SER SER HIS SER LEU ARG TYR PHE HIS THR ALA MET SEQRES 2 A 278 SER ARG PRO GLY LEU GLY GLU PRO ARG PHE ILE VAL VAL SEQRES 3 A 278 GLY TYR VAL ASP ASP THR GLN PHE VAL SER PHE ASP SER SEQRES 4 A 278 ASP SER GLU ASN PRO LYS MET GLU PRO ARG ALA ARG TRP SEQRES 5 A 278 MET GLU GLN GLU GLY PRO GLU TYR TRP GLU ARG GLU THR SEQRES 6 A 278 TRP LYS ALA ARG ASP MET GLY ARG ASN PHE ARG VAL ASN SEQRES 7 A 278 LEU ARG THR LEU LEU GLY TYR TYR ASN GLN SER LYS ASP SEQRES 8 A 278 GLU SER HIS THR LEU GLN TRP MET TYR GLY CYS ASP VAL SEQRES 9 A 278 GLY PRO ASP GLY ARG LEU LEU ARG GLY TYR CYS GLN GLU SEQRES 10 A 278 ALA TYR ASP GLY GLN ASP TYR ILE SER LEU ASN GLU ASP SEQRES 11 A 278 LEU ARG SER TRP THR ALA THR ASP PHE ALA SER GLN ILE SEQRES 12 A 278 SER LYS HIS LYS SER GLU MET VAL ASP GLU ALA HIS GLN SEQRES 13 A 278 GLN ARG ALA TYR LEU GLN GLY PRO CYS VAL GLU TRP LEU SEQRES 14 A 278 HIS THR TYR LEU ARG LEU GLY ASN LYS THR LEU LYS ARG SEQRES 15 A 278 SER ASP PRO PRO LYS ALA HIS VAL THR HIS HIS PRO ARG SEQRES 16 A 278 SER GLU ASP TYR VAL THR LEU ARG CYS TRP ALA LEU GLY SEQRES 17 A 278 PHE TYR PRO ALA ASP ILE THR LEU THR TRP GLN LEU ASN SEQRES 18 A 278 GLY GLU GLU LEU THR GLN ASP MET GLU PHE VAL GLU THR SEQRES 19 A 278 ARG PRO ALA GLY ASP GLY ASN PHE GLN LYS TRP ALA SER SEQRES 20 A 278 VAL VAL VAL PRO LEU GLY LYS GLU GLN ASN TYR THR CYS SEQRES 21 A 278 HIS VAL GLU HIS GLU GLY LEU PRO GLU PRO LEU THR LEU SEQRES 22 A 278 ARG TRP GLU PRO PRO SEQRES 1 B 99 ILE GLN LYS THR PRO GLN ILE GLN VAL TYR SER ARG HIS SEQRES 2 B 99 PRO PRO GLU ASN GLY LYS PRO ASN ILE LEU ASN CYS TYR SEQRES 3 B 99 VAL THR GLN PHE HIS PRO PRO HIS ILE GLU ILE GLN MET SEQRES 4 B 99 LEU LYS ASN GLY LYS LYS ILE PRO LYS VAL GLU MET SER SEQRES 5 B 99 ASP MET SER PHE SER LYS ASP TRP SER PHE TYR ILE LEU SEQRES 6 B 99 ALA HIS THR GLU PHE THR PRO THR GLU THR ASP THR TYR SEQRES 7 B 99 ALA CYS ARG VAL LYS HIS ALA SER MET ALA GLU PRO LYS SEQRES 8 B 99 THR VAL TYR TRP ASP ARG ASP MET SEQRES 1 P 9 ALA MET ALA PRO ARG THR LEU LEU LEU HET GOL A 301 6 HET GOL A 302 6 HET GOL A 303 6 HET NA A 304 1 HET NA A 305 1 HET NA A 306 1 HET NA A 307 1 HET NA A 308 1 HET NA A 309 1 HET GOL B 101 6 HETNAM GOL GLYCEROL HETNAM NA SODIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 GOL 4(C3 H8 O3) FORMUL 7 NA 6(NA 1+) FORMUL 14 HOH *120(H2 O) HELIX 1 AA1 ALA A 49 GLU A 55 5 7 HELIX 2 AA2 GLY A 56 ASN A 86 1 31 HELIX 3 AA3 ASP A 137 VAL A 150 1 14 HELIX 4 AA4 ASP A 151 GLY A 162 1 12 HELIX 5 AA5 GLY A 162 GLY A 175 1 14 HELIX 6 AA6 GLY A 175 LYS A 180 1 6 HELIX 7 AA7 LYS A 253 GLN A 255 5 3 SHEET 1 AA1 8 GLU A 46 PRO A 47 0 SHEET 2 AA1 8 THR A 31 ASP A 37 -1 N SER A 35 O GLU A 46 SHEET 3 AA1 8 ARG A 21 VAL A 28 -1 N VAL A 24 O PHE A 36 SHEET 4 AA1 8 HIS A 3 MET A 12 -1 N ARG A 6 O TYR A 27 SHEET 5 AA1 8 THR A 94 VAL A 103 -1 O TRP A 97 N HIS A 9 SHEET 6 AA1 8 LEU A 109 TYR A 118 -1 O LEU A 110 N ASP A 102 SHEET 7 AA1 8 GLN A 121 LEU A 126 -1 O LEU A 126 N CYS A 114 SHEET 8 AA1 8 TRP A 133 ALA A 135 -1 O THR A 134 N SER A 125 SHEET 1 AA2 4 LYS A 186 PRO A 193 0 SHEET 2 AA2 4 TYR A 198 PHE A 208 -1 O TRP A 204 N HIS A 188 SHEET 3 AA2 4 PHE A 241 PRO A 250 -1 O ALA A 245 N CYS A 203 SHEET 4 AA2 4 GLU A 229 PHE A 230 -1 N GLU A 229 O SER A 246 SHEET 1 AA3 4 LYS A 186 PRO A 193 0 SHEET 2 AA3 4 TYR A 198 PHE A 208 -1 O TRP A 204 N HIS A 188 SHEET 3 AA3 4 PHE A 241 PRO A 250 -1 O ALA A 245 N CYS A 203 SHEET 4 AA3 4 ARG A 234 PRO A 235 -1 N ARG A 234 O GLN A 242 SHEET 1 AA4 4 GLU A 222 GLU A 223 0 SHEET 2 AA4 4 THR A 214 LEU A 219 -1 N LEU A 219 O GLU A 222 SHEET 3 AA4 4 TYR A 257 GLU A 262 -1 O HIS A 260 N THR A 216 SHEET 4 AA4 4 LEU A 270 LEU A 272 -1 O LEU A 272 N CYS A 259 SHEET 1 AA5 4 GLN B 6 SER B 11 0 SHEET 2 AA5 4 ASN B 21 PHE B 30 -1 O ASN B 24 N TYR B 10 SHEET 3 AA5 4 PHE B 62 PHE B 70 -1 O ALA B 66 N CYS B 25 SHEET 4 AA5 4 GLU B 50 PHE B 56 -1 N SER B 52 O LEU B 65 SHEET 1 AA6 4 LYS B 44 LYS B 45 0 SHEET 2 AA6 4 GLU B 36 LYS B 41 -1 N LYS B 41 O LYS B 44 SHEET 3 AA6 4 TYR B 78 LYS B 83 -1 O ARG B 81 N GLN B 38 SHEET 4 AA6 4 LYS B 91 TYR B 94 -1 O LYS B 91 N VAL B 82 SSBOND 1 CYS A 101 CYS A 164 1555 1555 2.12 SSBOND 2 CYS A 203 CYS A 259 1555 1555 2.02 SSBOND 3 CYS B 25 CYS B 80 1555 1555 2.06 LINK OG1 THR A 10 NA NA A 305 1555 1555 3.01 LINK OD2 ASP A 29 NA NA A 304 1555 1555 2.60 LINK OG SER A 38 NA NA A 309 1555 1555 3.06 LINK OD1 ASP A 39 NA NA A 309 1555 1555 2.55 LINK OD1 ASN A 77 NA NA A 306 1555 1555 2.79 LINK OE2 GLU A 116 NA NA A 306 1555 1555 2.76 LINK OE1 GLN A 156 NA NA A 307 1555 1555 2.57 LINK O LEU A 179 NA NA A 304 1555 1555 2.64 LINK OH TYR A 209 NA NA A 304 1555 1555 2.89 LINK NA NA A 305 O MET B 54 1555 1555 2.88 LINK NA NA A 306 OG1 THR P 6 1555 1555 2.79 LINK NA NA A 306 O LEU P 7 1555 1555 2.96 CISPEP 1 TYR A 209 PRO A 210 0 3.81 CISPEP 2 HIS B 31 PRO B 32 0 3.98 SITE 1 AC1 4 ARG A 6 ASP A 29 ASP A 30 TYR B 63 SITE 1 AC2 7 LEU A 109 LEU A 110 ARG A 111 GLY A 112 SITE 2 AC2 7 GLU A 128 LEU A 130 GLN A 161 SITE 1 AC3 7 TYR A 85 ASN A 86 TYR A 118 ASP A 122 SITE 2 AC3 7 THR A 136 ASP A 137 HOH A 412 SITE 1 AC4 3 ASP A 29 LEU A 179 TYR A 209 SITE 1 AC5 3 PHE A 8 THR A 10 MET B 54 SITE 1 AC6 4 ASN A 77 GLU A 116 THR P 6 LEU P 7 SITE 1 AC7 2 TYR A 99 GLN A 156 SITE 1 AC8 1 SER A 2 SITE 1 AC9 3 ARG A 14 SER A 38 ASP A 39 SITE 1 AD1 7 ARG A 234 GLN B 8 VAL B 9 TYR B 94 SITE 2 AD1 7 ASP B 96 MET B 99 HOH B 201 CRYST1 67.207 75.876 105.211 90.00 90.00 90.00 P 21 2 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 0.014879 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013179 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009505 0.00000