PDB Short entry for 6FGP HEADER PROTEIN BINDING 11-JAN-18 6FGP TITLE NMR SOLUTION STRUCTURE OF MONOMERIC CCL5 IN COMPLEX WITH A DOUBLY- TITLE 2 SULFATED N-TERMINAL SEGMENT OF CCR5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: C-C CHEMOKINE RECEPTOR TYPE 5; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CCR5,CHEMR13,HIV-1 FUSION CORECEPTOR; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: N-TERMINAL SEGMENT OF CCR5, DOUBLY-SULFATED AT COMPND 7 POSITION Y10 AND Y14 THAT WERE SYNTHESIZED BY SOLID-PHASE PEPTIDE- COMPND 8 SYNTHESIS; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: C-C MOTIF CHEMOKINE 5; COMPND 11 CHAIN: B; COMPND 12 SYNONYM: EOCP,EOSINOPHIL CHEMOTACTIC CYTOKINE,SIS-DELTA,SMALL- COMPND 13 INDUCIBLE CYTOKINE A5,T CELL-SPECIFIC PROTEIN P228,TCP228,T-CELL- COMPND 14 SPECIFIC PROTEIN RANTES; COMPND 15 ENGINEERED: YES; COMPND 16 MUTATION: YES; COMPND 17 OTHER_DETAILS: CHEMOKINE PROTEIN (CONSIST P9S AND E66S MUTATIONS). SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 GENE: CCL5, D17S136E, SCYA5; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CHEMOKINE COMPLEX NMR, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.ANGLISTER,M.ABAYEV REVDAT 5 30-MAR-22 6FGP 1 REMARK REVDAT 4 11-SEP-19 6FGP 1 COMPND SOURCE REMARK DBREF REVDAT 4 2 1 SEQADV SEQRES HELIX SHEET REVDAT 4 3 1 SSBOND ATOM REVDAT 3 08-MAY-19 6FGP 1 REMARK REVDAT 2 13-JUN-18 6FGP 1 JRNL REVDAT 1 18-APR-18 6FGP 0 JRNL AUTH M.ABAYEV,J.P.G.L.M.RODRIGUES,G.SRIVASTAVA,B.ARSHAVA, JRNL AUTH 2 L.JAREMKO,M.JAREMKO,F.NAIDER,M.LEVITT,J.ANGLISTER JRNL TITL THE SOLUTION STRUCTURE OF MONOMERIC CCL5 IN COMPLEX WITH A JRNL TITL 2 DOUBLY SULFATED N-TERMINAL SEGMENT OF CCR5. JRNL REF FEBS J. V. 285 1988 2018 JRNL REFN ISSN 1742-4658 JRNL PMID 29619777 JRNL DOI 10.1111/FEBS.14460 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK REMARK 3 AUTHORS : BONVIN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6FGP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1200008183. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310; 310; 310 REMARK 210 PH : 4.8; 4.8; 4.8 REMARK 210 IONIC STRENGTH : 130; 130; 130 REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 120 UM [U-15N] CCL5(P9S)/NT REMARK 210 -CCR5(1-27), 90% H2O/10% D2O; REMARK 210 120 UM [U-13C] CCL5(P9S)/NT- REMARK 210 CCR5(1-27), 90% H2O/10% D2O; 120 REMARK 210 UM U-15N;13C CCL5(P9S)/NT-CCR5(1- REMARK 210 27), 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 HNCO; 3D HCCH-TOCSY; 3D CCH- REMARK 210 TOCSY; 3D HCC(CO)NH-TOCSY; 3D 1H- REMARK 210 15N TOCSY; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 13C NOESY AROMATIC; 2D 1H-1H REMARK 210 NOESY (DOUBLE FILTER); 2D 1H-1H REMARK 210 TOCSY (DOUBLE FILTER); 3D 1H-13C REMARK 210 NOESY (EDITED/FILTERED) REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW, XPLOR-NIH, CYANA REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 106 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: 1070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 GLY B 0 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 1 SER A 7 93.75 66.20 REMARK 500 1 TYS A 10 -55.29 70.82 REMARK 500 1 ILE A 12 -114.12 -87.93 REMARK 500 1 GLU A 18 -57.27 -135.80 REMARK 500 1 THR B 30 -77.94 -65.99 REMARK 500 1 SER B 31 -20.83 -146.73 REMARK 500 1 SER B 66 -71.08 -86.69 REMARK 500 2 SER A 7 81.22 60.88 REMARK 500 2 TYS A 10 -62.47 71.76 REMARK 500 2 ILE A 12 -119.37 -102.07 REMARK 500 2 THR B 30 -80.43 -58.65 REMARK 500 2 SER B 31 -33.57 -141.60 REMARK 500 3 TYS A 10 -59.68 67.46 REMARK 500 3 ILE A 12 -108.15 -93.94 REMARK 500 3 ASN A 13 -71.27 -25.81 REMARK 500 3 ASN A 24 79.69 59.21 REMARK 500 3 LYS A 26 66.51 65.22 REMARK 500 3 THR B 30 -80.67 -87.64 REMARK 500 3 THR B 43 -167.76 -79.05 REMARK 500 3 MET B 67 171.17 41.77 REMARK 500 4 SER A 7 97.20 63.99 REMARK 500 4 TYS A 10 -49.56 72.13 REMARK 500 4 ILE A 12 -111.66 -96.51 REMARK 500 4 SER B 31 -41.90 -161.87 REMARK 500 5 SER A 7 85.53 60.03 REMARK 500 5 TYS A 10 -52.98 71.72 REMARK 500 5 ILE A 12 -115.02 -97.45 REMARK 500 5 SER B 31 -33.15 -148.49 REMARK 500 6 SER A 7 82.31 51.44 REMARK 500 6 TYS A 10 -52.77 71.52 REMARK 500 6 ILE A 12 -121.52 -96.11 REMARK 500 6 PRO A 19 4.27 -69.75 REMARK 500 6 THR B 30 -72.95 -62.48 REMARK 500 6 SER B 31 -24.70 -151.61 REMARK 500 7 TYS A 10 -65.48 68.31 REMARK 500 7 ILE A 12 -97.30 -92.18 REMARK 500 7 ASN A 24 94.54 67.88 REMARK 500 7 THR B 30 -74.96 -79.23 REMARK 500 7 SER B 66 72.92 -152.29 REMARK 500 7 MET B 67 170.07 42.64 REMARK 500 8 TYR A 3 85.06 59.39 REMARK 500 8 TYS A 10 -47.42 72.50 REMARK 500 8 ILE A 12 -117.39 -102.83 REMARK 500 8 ASN A 13 -65.80 -22.65 REMARK 500 8 SER A 17 46.58 -79.59 REMARK 500 8 GLU A 18 36.94 -142.82 REMARK 500 8 ILE A 23 -150.84 -115.32 REMARK 500 8 VAL A 25 147.92 71.28 REMARK 500 8 LYS A 26 35.16 -79.21 REMARK 500 8 TYR B 3 159.52 68.87 REMARK 500 REMARK 500 THIS ENTRY HAS 77 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2L87 RELATED DB: PDB REMARK 900 PDB NT-CCR5 IN A TERNARY COMPLEX WITH HIV-1 GP120 AND A CD4-MIMIC REMARK 900 PEPTIDE REMARK 900 RELATED ID: 34232 RELATED DB: BMRB REMARK 900 NMR SOLUTION STRUCTURE OF MONOMERIC CCL5 IN COMPLEX WITH A DOUBLY- REMARK 900 SULFATED N-TERMINAL SEGMENT OF CCR5 DBREF 6FGP A 1 27 UNP P51681 CCR5_HUMAN 1 27 DBREF 6FGP B 1 68 UNP P13501 CCL5_HUMAN 24 91 SEQADV 6FGP ALA A 20 UNP P51681 CYS 20 CONFLICT SEQADV 6FGP GLY B 0 UNP P13501 EXPRESSION TAG SEQADV 6FGP SER B 9 UNP P13501 PRO 32 ENGINEERED MUTATION SEQADV 6FGP SER B 66 UNP P13501 GLU 89 ENGINEERED MUTATION SEQRES 1 A 27 MET ASP TYR GLN VAL SER SER PRO ILE TYS ASP ILE ASN SEQRES 2 A 27 TYS TYR THR SER GLU PRO ALA GLN LYS ILE ASN VAL LYS SEQRES 3 A 27 GLN SEQRES 1 B 69 GLY SER PRO TYR SER SER ASP THR THR SER CYS CYS PHE SEQRES 2 B 69 ALA TYR ILE ALA ARG PRO LEU PRO ARG ALA HIS ILE LYS SEQRES 3 B 69 GLU TYR PHE TYR THR SER GLY LYS CYS SER ASN PRO ALA SEQRES 4 B 69 VAL VAL PHE VAL THR ARG LYS ASN ARG GLN VAL CYS ALA SEQRES 5 B 69 ASN PRO GLU LYS LYS TRP VAL ARG GLU TYR ILE ASN SER SEQRES 6 B 69 LEU SER MET SER MODRES 6FGP TYS A 10 TYR MODIFIED RESIDUE MODRES 6FGP TYS A 14 TYR MODIFIED RESIDUE HET TYS A 10 24 HET TYS A 14 24 HETNAM TYS O-SULFO-L-TYROSINE FORMUL 1 TYS 2(C9 H11 N O6 S) HELIX 1 AA1 ILE A 12 THR A 16 5 5 HELIX 2 AA2 PRO B 20 ILE B 24 5 5 HELIX 3 AA3 LYS B 55 MET B 67 1 13 SHEET 1 AA1 3 GLU B 26 TYR B 29 0 SHEET 2 AA1 3 VAL B 39 VAL B 42 -1 O VAL B 40 N PHE B 28 SHEET 3 AA1 3 VAL B 49 ALA B 51 -1 O ALA B 51 N VAL B 39 SSBOND 1 CYS B 10 CYS B 34 1555 1555 2.03 SSBOND 2 CYS B 11 CYS B 50 1555 1555 2.03 LINK C ILE A 9 N TYS A 10 1555 1555 1.33 LINK C TYS A 10 N ASP A 11 1555 1555 1.33 LINK C ASN A 13 N TYS A 14 1555 1555 1.33 LINK C TYS A 14 N TYR A 15 1555 1555 1.33 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000