HEADER IMMUNE SYSTEM 11-SEP-17 5YD5 TITLE CRYSTAL STRUCTURE OF THE SCFV ANTIBODY 4B08 WITH EPITOPE PEPTIDE TITLE 2 (MUTATION N3A) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SCFV 4B08; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PEPTIDE EPITOPE (MUTATION N3A); COMPND 7 CHAIN: B, D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_TAXID: 10090; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS ANTIBODY, BIOMOLECULAR RECOGNITION, MD SIMULATIONS, THERMODYNAMICS, KEYWDS 2 IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR J.M.M.CAAVEIRO,K.MIYANABE,K.TSUMOTO REVDAT 3 22-NOV-23 5YD5 1 REMARK REVDAT 2 04-JUL-18 5YD5 1 JRNL REVDAT 1 06-JUN-18 5YD5 0 JRNL AUTH K.MIYANABE,H.AKIBA,D.KURODA,M.NAKAKIDO,O.KUSANO-ARAI, JRNL AUTH 2 H.IWANARI,T.HAMAKUBO,J.M.M.CAAVEIRO,K.TSUMOTO JRNL TITL INTRAMOLECULAR H-BONDS GOVERN THE RECOGNITION OF A FLEXIBLE JRNL TITL 2 PEPTIDE BY AN ANTIBODY JRNL REF J. BIOCHEM. V. 164 65 2018 JRNL REFN ISSN 1756-2651 JRNL PMID 29924367 JRNL DOI 10.1093/JB/MVY032 REMARK 2 REMARK 2 RESOLUTION. 1.96 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) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 38732 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) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1584 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) : 1.96 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.01 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2568 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.50 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE SET COUNT : 104 REMARK 3 BIN FREE R VALUE : 0.3110 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3845 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 359 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.91000 REMARK 3 B22 (A**2) : 10.00000 REMARK 3 B33 (A**2) : -7.09000 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): 0.039 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.037 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.088 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.994 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4013 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3483 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5448 ; 1.548 ; 1.953 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8109 ; 0.951 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 514 ; 6.906 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 164 ;29.592 ;23.171 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 617 ;12.083 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;19.597 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 574 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4521 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 872 ; 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): 2035 ; 1.122 ; 1.559 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2034 ; 1.121 ; 1.559 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2538 ; 1.818 ; 2.327 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2539 ; 1.818 ; 2.327 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1977 ; 1.680 ; 1.678 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1945 ; 1.586 ; 1.642 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2856 ; 2.520 ; 2.392 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4529 ; 4.282 ;17.907 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4473 ; 4.156 ;17.729 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 5YD5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1300005063. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAY-15 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 : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NE3A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40361 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 REMARK 200 RESOLUTION RANGE LOW (A) : 37.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.12900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.1 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.42500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.700 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: 5YD3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM BIS-TRIS 1.8 M AMMONIUM REMARK 280 SULPHATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.95000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.11000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.95000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 57.11000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 522 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 DIMERIC MEANS ONE CHAIN REMARK 400 OF ANTIBODY AND ONE CHAIN OF PEPTIDE REMARK 400 REMARK 400 A + B REMARK 400 OR REMARK 400 C + D 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 ASP B 1 REMARK 465 GLY C 129 REMARK 465 SER C 130 REMARK 465 GLY C 131 REMARK 465 GLY C 132 REMARK 465 GLY C 133 REMARK 465 GLY C 134 REMARK 465 SER C 135 REMARK 465 GLY C 136 REMARK 465 GLY C 137 REMARK 465 GLY C 138 REMARK 465 VAL C 253 REMARK 465 ASP D 1 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 A 104 -6.89 90.70 REMARK 500 SER A 135 -167.05 -169.41 REMARK 500 MET A 196 -45.83 81.05 REMARK 500 THR C 104 -10.58 89.73 REMARK 500 MET C 196 -46.31 80.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 C 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 C 303 DBREF 5YD5 A 3 253 PDB 5YD5 5YD5 3 253 DBREF 5YD5 B 1 9 PDB 5YD5 5YD5 1 9 DBREF 5YD5 C 3 253 PDB 5YD5 5YD5 3 253 DBREF 5YD5 D 1 9 PDB 5YD5 5YD5 1 9 SEQRES 1 A 251 GLU VAL GLN LEU GLN GLN SER GLY ALA GLU LEU VAL ARG SEQRES 2 A 251 PRO GLY THR SER VAL LYS MET SER CYS LYS ALA ALA GLY SEQRES 3 A 251 TYR THR PHE THR LYS TYR TRP ILE GLY TRP VAL LYS GLN SEQRES 4 A 251 ARG PRO GLY HIS GLY LEU GLU TRP ILE GLY ASP ILE HIS SEQRES 5 A 251 PRO GLY SER PHE TYR SER ASN TYR ASN GLU LYS PHE LYS SEQRES 6 A 251 GLY LYS ALA THR LEU THR ALA ASP THR SER SER SER THR SEQRES 7 A 251 ALA TYR MET GLN LEU SER SER LEU THR SER GLU ASP SER SEQRES 8 A 251 ALA ILE TYR TYR CYS ALA ARG ASP TYR TYR THR ASN TYR SEQRES 9 A 251 GLY ASP TRP GLY GLN GLY THR SER VAL THR VAL SER SER SEQRES 10 A 251 ALA GLY GLY GLY GLY SER GLY GLY GLY GLY SER GLY GLY SEQRES 11 A 251 GLY GLY SER GLY GLY GLY GLY SER ASP ILE VAL MET THR SEQRES 12 A 251 GLN ALA ALA PRO SER VAL SER VAL THR PRO GLY GLU SER SEQRES 13 A 251 VAL SER ILE SER CYS ARG SER SER LYS SER LEU LEU HIS SEQRES 14 A 251 ARG ASN GLY ASN THR TYR LEU PHE TRP PHE LEU GLN ARG SEQRES 15 A 251 PRO GLY GLN SER PRO GLN LEU LEU ILE TYR ARG MET SER SEQRES 16 A 251 ASN LEU ALA SER GLY VAL PRO ASP ARG PHE SER GLY SER SEQRES 17 A 251 GLY SER GLY THR ALA PHE THR LEU ARG ILE SER ARG VAL SEQRES 18 A 251 GLU ALA GLU ASP VAL GLY VAL TYR TYR CYS MET GLN HIS SEQRES 19 A 251 LEU GLU TYR PRO TYR THR PHE GLY SER GLY THR LYS LEU SEQRES 20 A 251 GLU LEU LYS VAL SEQRES 1 B 9 ASP ILE ALA TYR TYR THR SER GLU PRO SEQRES 1 C 251 GLU VAL GLN LEU GLN GLN SER GLY ALA GLU LEU VAL ARG SEQRES 2 C 251 PRO GLY THR SER VAL LYS MET SER CYS LYS ALA ALA GLY SEQRES 3 C 251 TYR THR PHE THR LYS TYR TRP ILE GLY TRP VAL LYS GLN SEQRES 4 C 251 ARG PRO GLY HIS GLY LEU GLU TRP ILE GLY ASP ILE HIS SEQRES 5 C 251 PRO GLY SER PHE TYR SER ASN TYR ASN GLU LYS PHE LYS SEQRES 6 C 251 GLY LYS ALA THR LEU THR ALA ASP THR SER SER SER THR SEQRES 7 C 251 ALA TYR MET GLN LEU SER SER LEU THR SER GLU ASP SER SEQRES 8 C 251 ALA ILE TYR TYR CYS ALA ARG ASP TYR TYR THR ASN TYR SEQRES 9 C 251 GLY ASP TRP GLY GLN GLY THR SER VAL THR VAL SER SER SEQRES 10 C 251 ALA GLY GLY GLY GLY SER GLY GLY GLY GLY SER GLY GLY SEQRES 11 C 251 GLY GLY SER GLY GLY GLY GLY SER ASP ILE VAL MET THR SEQRES 12 C 251 GLN ALA ALA PRO SER VAL SER VAL THR PRO GLY GLU SER SEQRES 13 C 251 VAL SER ILE SER CYS ARG SER SER LYS SER LEU LEU HIS SEQRES 14 C 251 ARG ASN GLY ASN THR TYR LEU PHE TRP PHE LEU GLN ARG SEQRES 15 C 251 PRO GLY GLN SER PRO GLN LEU LEU ILE TYR ARG MET SER SEQRES 16 C 251 ASN LEU ALA SER GLY VAL PRO ASP ARG PHE SER GLY SER SEQRES 17 C 251 GLY SER GLY THR ALA PHE THR LEU ARG ILE SER ARG VAL SEQRES 18 C 251 GLU ALA GLU ASP VAL GLY VAL TYR TYR CYS MET GLN HIS SEQRES 19 C 251 LEU GLU TYR PRO TYR THR PHE GLY SER GLY THR LYS LEU SEQRES 20 C 251 GLU LEU LYS VAL SEQRES 1 D 9 ASP ILE ALA TYR TYR THR SER GLU PRO HET SO4 A 301 5 HET SO4 A 302 5 HET SO4 A 303 5 HET SO4 A 304 5 HET SO4 A 305 5 HET SO4 C 301 5 HET SO4 C 302 5 HET SO4 C 303 5 HETNAM SO4 SULFATE ION FORMUL 5 SO4 8(O4 S 2-) FORMUL 13 HOH *359(H2 O) HELIX 1 AA1 GLU A 64 LYS A 67 5 4 HELIX 2 AA2 THR A 89 SER A 93 5 5 HELIX 3 AA3 GLU A 224 VAL A 228 5 5 HELIX 4 AA4 THR C 30 TYR C 34 5 5 HELIX 5 AA5 GLU C 64 LYS C 67 5 4 HELIX 6 AA6 THR C 89 SER C 93 5 5 HELIX 7 AA7 GLU C 224 VAL C 228 5 5 SHEET 1 AA1 4 GLN A 5 GLN A 8 0 SHEET 2 AA1 4 VAL A 20 ALA A 27 -1 O LYS A 25 N GLN A 7 SHEET 3 AA1 4 THR A 80 LEU A 85 -1 O MET A 83 N MET A 22 SHEET 4 AA1 4 ALA A 70 ASP A 75 -1 N ASP A 75 O THR A 80 SHEET 1 AA2 6 GLU A 12 VAL A 14 0 SHEET 2 AA2 6 THR A 113 VAL A 117 1 O SER A 114 N GLU A 12 SHEET 3 AA2 6 ALA A 94 TYR A 102 -1 N ALA A 94 O VAL A 115 SHEET 4 AA2 6 ILE A 36 GLN A 41 -1 N GLN A 41 O ILE A 95 SHEET 5 AA2 6 LEU A 47 ILE A 53 -1 O ILE A 50 N TRP A 38 SHEET 6 AA2 6 SER A 60 TYR A 62 -1 O ASN A 61 N ASP A 52 SHEET 1 AA3 4 GLU A 12 VAL A 14 0 SHEET 2 AA3 4 THR A 113 VAL A 117 1 O SER A 114 N GLU A 12 SHEET 3 AA3 4 ALA A 94 TYR A 102 -1 N ALA A 94 O VAL A 115 SHEET 4 AA3 4 ASN A 105 TRP A 109 -1 O ASN A 105 N TYR A 102 SHEET 1 AA4 4 MET A 144 THR A 145 0 SHEET 2 AA4 4 VAL A 159 SER A 165 -1 O ARG A 164 N THR A 145 SHEET 3 AA4 4 ALA A 215 ILE A 220 -1 O ILE A 220 N VAL A 159 SHEET 4 AA4 4 PHE A 207 GLY A 211 -1 N SER A 208 O ARG A 219 SHEET 1 AA5 6 SER A 150 VAL A 153 0 SHEET 2 AA5 6 THR A 247 LEU A 251 1 O LYS A 248 N VAL A 151 SHEET 3 AA5 6 GLY A 229 GLN A 235 -1 N GLY A 229 O LEU A 249 SHEET 4 AA5 6 LEU A 178 GLN A 183 -1 N PHE A 181 O TYR A 232 SHEET 5 AA5 6 GLN A 190 TYR A 194 -1 O LEU A 192 N TRP A 180 SHEET 6 AA5 6 ASN A 198 LEU A 199 -1 O ASN A 198 N TYR A 194 SHEET 1 AA6 4 SER A 150 VAL A 153 0 SHEET 2 AA6 4 THR A 247 LEU A 251 1 O LYS A 248 N VAL A 151 SHEET 3 AA6 4 GLY A 229 GLN A 235 -1 N GLY A 229 O LEU A 249 SHEET 4 AA6 4 THR A 242 PHE A 243 -1 O THR A 242 N GLN A 235 SHEET 1 AA7 4 GLN C 5 GLN C 8 0 SHEET 2 AA7 4 VAL C 20 ALA C 27 -1 O LYS C 25 N GLN C 7 SHEET 3 AA7 4 THR C 80 LEU C 85 -1 O MET C 83 N MET C 22 SHEET 4 AA7 4 ALA C 70 ASP C 75 -1 N ASP C 75 O THR C 80 SHEET 1 AA8 6 GLU C 12 VAL C 14 0 SHEET 2 AA8 6 THR C 113 VAL C 117 1 O SER C 114 N GLU C 12 SHEET 3 AA8 6 ALA C 94 TYR C 102 -1 N ALA C 94 O VAL C 115 SHEET 4 AA8 6 ILE C 36 GLN C 41 -1 N GLN C 41 O ILE C 95 SHEET 5 AA8 6 LEU C 47 ILE C 53 -1 O GLU C 48 N LYS C 40 SHEET 6 AA8 6 SER C 60 TYR C 62 -1 O ASN C 61 N ASP C 52 SHEET 1 AA9 4 GLU C 12 VAL C 14 0 SHEET 2 AA9 4 THR C 113 VAL C 117 1 O SER C 114 N GLU C 12 SHEET 3 AA9 4 ALA C 94 TYR C 102 -1 N ALA C 94 O VAL C 115 SHEET 4 AA9 4 ASN C 105 TRP C 109 -1 O ASN C 105 N TYR C 102 SHEET 1 AB1 4 MET C 144 THR C 145 0 SHEET 2 AB1 4 VAL C 159 SER C 165 -1 O ARG C 164 N THR C 145 SHEET 3 AB1 4 ALA C 215 ILE C 220 -1 O LEU C 218 N ILE C 161 SHEET 4 AB1 4 PHE C 207 GLY C 211 -1 N SER C 208 O ARG C 219 SHEET 1 AB2 6 SER C 150 VAL C 153 0 SHEET 2 AB2 6 THR C 247 LEU C 251 1 O LYS C 248 N VAL C 151 SHEET 3 AB2 6 GLY C 229 GLN C 235 -1 N GLY C 229 O LEU C 249 SHEET 4 AB2 6 LEU C 178 GLN C 183 -1 N PHE C 181 O TYR C 232 SHEET 5 AB2 6 GLN C 190 TYR C 194 -1 O LEU C 192 N TRP C 180 SHEET 6 AB2 6 ASN C 198 LEU C 199 -1 O ASN C 198 N TYR C 194 SHEET 1 AB3 4 SER C 150 VAL C 153 0 SHEET 2 AB3 4 THR C 247 LEU C 251 1 O LYS C 248 N VAL C 151 SHEET 3 AB3 4 GLY C 229 GLN C 235 -1 N GLY C 229 O LEU C 249 SHEET 4 AB3 4 THR C 242 PHE C 243 -1 O THR C 242 N GLN C 235 SSBOND 1 CYS A 24 CYS A 98 1555 1555 2.09 SSBOND 2 CYS A 163 CYS A 233 1555 1555 2.13 SSBOND 3 CYS C 24 CYS C 98 1555 1555 2.12 SSBOND 4 CYS C 163 CYS C 233 1555 1555 2.12 CISPEP 1 GLY A 134 SER A 135 0 11.70 CISPEP 2 TYR A 239 PRO A 240 0 -14.11 CISPEP 3 GLY C 127 GLY C 128 0 8.43 CISPEP 4 TYR C 239 PRO C 240 0 -11.27 SITE 1 AC1 7 ARG A 15 GLY A 122 GLY A 123 SER C 19 SITE 2 AC1 7 SER C 86 GLY C 127 GLY C 128 SITE 1 AC2 6 SER A 19 GLY A 127 GLY A 128 ARG C 15 SITE 2 AC2 6 GLY C 122 GLY C 123 SITE 1 AC3 6 SER A 158 ARG A 219 SER A 221 HOH A 406 SITE 2 AC3 6 HOH A 546 ARG C 172 SITE 1 AC4 5 GLY A 28 THR A 30 LYS A 33 TYR A 34 SITE 2 AC4 5 HOH A 457 SITE 1 AC5 2 SER A 118 SER A 119 SITE 1 AC6 5 ARG A 172 HOH B 103 SER C 158 ARG C 219 SITE 2 AC6 5 SER C 221 SITE 1 AC7 4 TYR C 29 THR C 30 LYS C 33 TYR C 34 SITE 1 AC8 3 THR A 154 SER C 118 SER C 119 CRYST1 61.620 81.900 114.220 90.00 90.00 90.00 P 2 21 21 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 0.016228 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012210 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008755 0.00000