HEADER IMMUNE SYSTEM 07-DEC-17 5YY4 TITLE CRYSTAL STRUCTURE OF THE SCFV ANTIBODY 4B08 WITH SULFATED EPITOPE TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SCFV 4B08; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: C-C CHEMOKINE RECEPTOR TYPE 5; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: CCR5,CHEMR13,HIV-1 FUSION CORECEPTOR; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_TAXID: 10090; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VARIANT: DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PRA2; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 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 5 16-OCT-24 5YY4 1 REMARK REVDAT 4 22-NOV-23 5YY4 1 REMARK REVDAT 3 01-AUG-18 5YY4 1 JRNL REVDAT 2 25-JUL-18 5YY4 1 JRNL REVDAT 1 18-JUL-18 5YY4 0 JRNL AUTH K.MIYANABE,T.YAMASHITA,Y.ABE,H.AKIBA,Y.TAKAMATSU,M.NAKAKIDO, JRNL AUTH 2 T.HAMAKUBO,T.UEDA,J.M.M.CAAVEIRO,K.TSUMOTO JRNL TITL TYROSINE SULFATION RESTRICTS THE CONFORMATIONAL ENSEMBLE OF JRNL TITL 2 A FLEXIBLE PEPTIDE, STRENGTHENING THE BINDING AFFINITY FOR JRNL TITL 3 AN ANTIBODY JRNL REF BIOCHEMISTRY V. 57 4177 2018 JRNL REFN ISSN 1520-4995 JRNL PMID 29936828 JRNL DOI 10.1021/ACS.BIOCHEM.8B00592 REMARK 2 REMARK 2 RESOLUTION. 1.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 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) : 1.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 31928 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) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1007 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) : 1.59 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.63 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2116 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.2270 REMARK 3 BIN FREE R VALUE SET COUNT : 70 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1899 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 266 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.60000 REMARK 3 B22 (A**2) : 0.27000 REMARK 3 B33 (A**2) : -0.87000 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): 0.080 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.084 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.055 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.568 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2048 ; 0.013 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1788 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2804 ; 1.597 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4183 ; 0.953 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 274 ; 6.320 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 87 ;32.903 ;23.218 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 330 ;10.714 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;20.613 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 299 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2319 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 450 ; 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): 1007 ; 1.290 ; 1.810 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1006 ; 1.290 ; 1.810 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1262 ; 1.967 ; 2.706 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1263 ; 1.967 ; 2.706 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1041 ; 2.205 ; 2.081 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1033 ; 2.179 ; 2.067 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1513 ; 3.560 ; 3.016 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2271 ; 5.286 ;21.648 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2210 ; 5.148 ;20.982 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 5YY4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1300006119. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A 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 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM 7.2.1 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 7.0.046 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32983 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.590 REMARK 200 RESOLUTION RANGE LOW (A) : 26.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 9.400 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.8 REMARK 200 DATA REDUNDANCY IN SHELL : 9.20 REMARK 200 R MERGE FOR SHELL (I) : 0.83100 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 2.7.17 REMARK 200 STARTING MODEL: 5YD3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM SODIUM ACETATE, 1.4M AMMONIUM REMARK 280 SULFATE, PH 4.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 22.62500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.96000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.30500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.96000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.62500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.30500 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 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 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 ALA A 120 REMARK 465 GLY A 121 REMARK 465 GLY A 122 REMARK 465 GLY A 123 REMARK 465 GLY A 124 REMARK 465 SER A 125 REMARK 465 GLY A 126 REMARK 465 GLY A 127 REMARK 465 GLY A 128 REMARK 465 GLY A 129 REMARK 465 SER A 130 REMARK 465 GLY A 131 REMARK 465 GLY A 132 REMARK 465 GLY A 133 REMARK 465 GLY A 134 REMARK 465 SER A 135 REMARK 465 ASP B 1 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 O2 SO4 A 302 O HOH A 401 2.14 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 195 NE - CZ - NH2 ANGL. DEV. = 3.0 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 A 104 -8.21 87.63 REMARK 500 MET A 196 -48.49 78.23 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 CL A 303 DBREF 5YY4 A 3 254 PDB 5YY4 5YY4 3 254 DBREF 5YY4 B 1 9 UNP P51681 CCR5_HUMAN 11 19 SEQRES 1 A 252 GLU VAL GLN LEU GLN GLN SER GLY ALA GLU LEU VAL ARG SEQRES 2 A 252 PRO GLY THR SER VAL LYS MET SER CYS LYS ALA ALA GLY SEQRES 3 A 252 TYR THR PHE THR LYS TYR TRP ILE GLY TRP VAL LYS GLN SEQRES 4 A 252 ARG PRO GLY HIS GLY LEU GLU TRP ILE GLY ASP ILE HIS SEQRES 5 A 252 PRO GLY SER PHE TYR SER ASN TYR ASN GLU LYS PHE LYS SEQRES 6 A 252 GLY LYS ALA THR LEU THR ALA ASP THR SER SER SER THR SEQRES 7 A 252 ALA TYR MET GLN LEU SER SER LEU THR SER GLU ASP SER SEQRES 8 A 252 ALA ILE TYR TYR CYS ALA ARG ASP TYR TYR THR ASN TYR SEQRES 9 A 252 GLY ASP TRP GLY GLN GLY THR SER VAL THR VAL SER SER SEQRES 10 A 252 ALA GLY GLY GLY GLY SER GLY GLY GLY GLY SER GLY GLY SEQRES 11 A 252 GLY GLY SER GLY GLY GLY GLY SER ASP ILE VAL MET THR SEQRES 12 A 252 GLN ALA ALA PRO SER VAL SER VAL THR PRO GLY GLU SER SEQRES 13 A 252 VAL SER ILE SER CYS ARG SER SER LYS SER LEU LEU HIS SEQRES 14 A 252 ARG ASN GLY ASN THR TYR LEU PHE TRP PHE LEU GLN ARG SEQRES 15 A 252 PRO GLY GLN SER PRO GLN LEU LEU ILE TYR ARG MET SER SEQRES 16 A 252 ASN LEU ALA SER GLY VAL PRO ASP ARG PHE SER GLY SER SEQRES 17 A 252 GLY SER GLY THR ALA PHE THR LEU ARG ILE SER ARG VAL SEQRES 18 A 252 GLU ALA GLU ASP VAL GLY VAL TYR TYR CYS MET GLN HIS SEQRES 19 A 252 LEU GLU TYR PRO TYR THR PHE GLY SER GLY THR LYS LEU SEQRES 20 A 252 GLU LEU LYS VAL ARG SEQRES 1 B 9 ASP ILE ASN TYS TYS THR SER GLU PRO MODRES 5YY4 TYS B 4 TYR MODIFIED RESIDUE MODRES 5YY4 TYS B 5 TYR MODIFIED RESIDUE HET TYS B 4 16 HET TYS B 5 16 HET SO4 A 301 5 HET SO4 A 302 5 HET CL A 303 1 HETNAM TYS O-SULFO-L-TYROSINE HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION FORMUL 2 TYS 2(C9 H11 N O6 S) FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 CL CL 1- FORMUL 6 HOH *266(H2 O) HELIX 1 AA1 THR A 30 TYR A 34 5 5 HELIX 2 AA2 GLU A 64 LYS A 67 5 4 HELIX 3 AA3 THR A 89 SER A 93 5 5 HELIX 4 AA4 GLU A 224 VAL A 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 LEU A 85 N VAL A 20 SHEET 4 AA1 4 ALA A 70 ASP A 75 -1 N THR A 71 O GLN A 84 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 GLU A 48 N LYS A 40 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 PHE A 216 N CYS A 163 SHEET 4 AA4 4 PHE A 207 SER A 212 -1 N SER A 212 O ALA A 215 SHEET 1 AA5 6 SER A 150 VAL A 153 0 SHEET 2 AA5 6 THR A 247 LEU A 251 1 O GLU A 250 N VAL A 153 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 179 O MET A 234 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 GLU A 250 N VAL A 153 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 SSBOND 1 CYS A 24 CYS A 98 1555 1555 2.06 SSBOND 2 CYS A 163 CYS A 233 1555 1555 2.08 LINK C ASN B 3 N TYS B 4 1555 1555 1.33 LINK C TYS B 4 N TYS B 5 1555 1555 1.33 LINK C TYS B 5 N THR B 6 1555 1555 1.33 CISPEP 1 TYR A 239 PRO A 240 0 -9.37 SITE 1 AC1 7 TYR A 29 THR A 30 LYS A 33 TYR A 34 SITE 2 AC1 7 ARG A 184 HOH A 454 HOH A 583 SITE 1 AC2 7 SER A 210 GLY A 211 ARG A 219 HOH A 401 SITE 2 AC2 7 HOH A 541 HOH A 557 HOH A 575 SITE 1 AC3 5 GLY A 138 GLY A 139 SER A 140 SER A 158 SITE 2 AC3 5 HOH A 596 CRYST1 45.250 56.610 97.920 90.00 90.00 90.00 P 21 21 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 0.022099 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017665 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010212 0.00000