HEADER PEPTIDE BINDING PROTEIN 27-JUL-17 5OLF TITLE LIGAND-BASED NMR STUDY OF C-X-C CHEMOKINE RECEPTOR TYPE 4 (CXCR4)- TITLE 2 LIGAND INTERACTIONS IN LIVING CANCER CELLS COMPND MOL_ID: 1; COMPND 2 MOLECULE: GBA-ALA-CYS-ARG-PHE-PHE-CYS; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS CXCR4, PEPTIDE BINDING PROTEIN, IN-CELL NMR EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR D.BRANCACCIO,A.CAROTENUTO REVDAT 3 23-OCT-24 5OLF 1 REMARK REVDAT 2 15-MAY-19 5OLF 1 ATOM REVDAT 1 06-JUN-18 5OLF 0 JRNL AUTH D.BRANCACCIO,D.DIANA,S.DI MARO,F.S.DI LEVA,S.TOMASSI, JRNL AUTH 2 R.FATTORUSSO,L.RUSSO,S.SCALA,A.M.TROTTA,L.PORTELLA, JRNL AUTH 3 E.NOVELLINO,L.MARINELLI,A.CAROTENUTO JRNL TITL LIGAND-BASED NMR STUDY OF C-X-C CHEMOKINE RECEPTOR TYPE 4 JRNL TITL 2 (CXCR4)-LIGAND INTERACTIONS ON LIVING CANCER CELLS. JRNL REF J. MED. CHEM. V. 61 2910 2018 JRNL REFN ISSN 1520-4804 JRNL PMID 29522685 JRNL DOI 10.1021/ACS.JMEDCHEM.7B01830 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA REMARK 3 AUTHORS : GUNTERT, BRAUN AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5OLF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1200005994. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2.0 MM NA PEPTIDE, 10 % [U-99% REMARK 210 2H] D2O, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR, XEASY REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 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 1 CYS A 7 C CYS A 7 O 0.135 REMARK 500 1 CYS A 7 C CYS A 7 OXT 0.126 REMARK 500 2 CYS A 7 C CYS A 7 O 0.135 REMARK 500 2 CYS A 7 C CYS A 7 OXT 0.126 REMARK 500 3 CYS A 7 C CYS A 7 O 0.135 REMARK 500 3 CYS A 7 C CYS A 7 OXT 0.126 REMARK 500 4 CYS A 7 C CYS A 7 O 0.134 REMARK 500 4 CYS A 7 C CYS A 7 OXT 0.126 REMARK 500 5 CYS A 7 C CYS A 7 O 0.135 REMARK 500 5 CYS A 7 C CYS A 7 OXT 0.126 REMARK 500 6 CYS A 7 C CYS A 7 O 0.134 REMARK 500 6 CYS A 7 C CYS A 7 OXT 0.126 REMARK 500 7 CYS A 7 C CYS A 7 O 0.134 REMARK 500 7 CYS A 7 C CYS A 7 OXT 0.126 REMARK 500 8 CYS A 7 C CYS A 7 O 0.134 REMARK 500 8 CYS A 7 C CYS A 7 OXT 0.126 REMARK 500 9 CYS A 7 C CYS A 7 O 0.134 REMARK 500 9 CYS A 7 C CYS A 7 OXT 0.126 REMARK 500 10 CYS A 7 C CYS A 7 O 0.135 REMARK 500 10 CYS A 7 C CYS A 7 OXT 0.126 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 1 ARG A 4 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 ARG A 4 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 ARG A 4 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 4 ARG A 4 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 5 ARG A 4 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 ARG A 4 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 7 ARG A 4 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 8 ARG A 4 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 9 ARG A 4 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 10 ARG A 4 NE - CZ - NH2 ANGL. DEV. = 3.2 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 1 ALA A 2 119.98 59.08 REMARK 500 1 CYS A 3 -58.97 -121.29 REMARK 500 1 PHE A 5 -70.65 -140.95 REMARK 500 2 CYS A 3 -60.50 -127.31 REMARK 500 2 PHE A 5 -70.18 -140.61 REMARK 500 3 CYS A 3 -59.04 -128.06 REMARK 500 3 PHE A 5 -70.51 -138.93 REMARK 500 4 CYS A 3 -60.03 -106.47 REMARK 500 4 PHE A 5 -70.32 -142.02 REMARK 500 5 ALA A 2 108.91 -44.95 REMARK 500 5 PHE A 5 -70.58 -142.30 REMARK 500 6 CYS A 3 -60.33 -105.24 REMARK 500 6 PHE A 5 -70.48 -138.31 REMARK 500 7 ALA A 2 70.07 41.27 REMARK 500 7 PHE A 5 -64.68 -135.48 REMARK 500 7 PHE A 6 -52.93 -126.97 REMARK 500 8 ALA A 2 70.58 53.43 REMARK 500 8 PHE A 5 -65.64 -134.81 REMARK 500 8 PHE A 6 -68.18 -122.46 REMARK 500 9 ALA A 2 70.22 40.62 REMARK 500 9 PHE A 5 -64.86 -135.49 REMARK 500 9 PHE A 6 -52.94 -126.86 REMARK 500 10 ALA A 2 87.28 176.59 REMARK 500 10 PHE A 5 -64.30 -136.74 REMARK 500 10 PHE A 6 -52.87 -127.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34166 RELATED DB: BMRB REMARK 900 LIGAND-BASED NMR STUDY OF C-X-C CHEMOKINE RECEPTOR TYPE 4 (CXCR4)- REMARK 900 LIGAND INTERACTIONS IN LIVING CANCER CELLS DBREF 5OLF A 1 7 PDB 5OLF 5OLF 1 7 SEQRES 1 A 7 9XQ ALA CYS ARG PHE PHE CYS HET 9XQ A 1 21 HETNAM 9XQ [AZANYL-[(3-CARBOXYPHENYL)AMINO]METHYLIDENE]AZANIUM FORMUL 1 9XQ C8 H10 N3 O2 1+ SSBOND 1 CYS A 3 CYS A 7 1555 1555 2.00 LINK C 9XQ A 1 N ALA A 2 1555 1555 1.36 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 MODEL 1 HETATM 1 CG 9XQ A 1 3.196 -7.468 -2.307 1.00 0.00 C HETATM 2 CD1 9XQ A 1 4.432 -7.445 -1.634 1.00 0.00 C HETATM 3 CE1 9XQ A 1 4.805 -8.483 -0.771 1.00 0.00 C HETATM 4 CZ 9XQ A 1 3.905 -9.535 -0.550 1.00 0.00 C HETATM 5 CE2 9XQ A 1 2.672 -9.559 -1.185 1.00 0.00 C HETATM 6 CD2 9XQ A 1 2.327 -8.540 -2.062 1.00 0.00 C HETATM 7 NH1 9XQ A 1 6.395 -10.131 1.398 1.00 0.00 N HETATM 8 NH2 9XQ A 1 8.122 -8.845 0.874 1.00 0.00 N HETATM 9 C 9XQ A 1 2.750 -6.414 -3.302 1.00 0.00 C HETATM 10 O 9XQ A 1 1.885 -6.691 -4.135 1.00 0.00 O HETATM 11 NE3 9XQ A 1 6.151 -8.444 -0.203 1.00 0.00 N HETATM 12 CE4 9XQ A 1 6.866 -9.147 0.681 1.00 0.00 C HETATM 13 HD1 9XQ A 1 5.109 -6.628 -1.838 1.00 0.00 H HETATM 14 HZ 9XQ A 1 4.137 -10.382 0.077 1.00 0.00 H HETATM 15 HE2 9XQ A 1 1.980 -10.375 -1.018 1.00 0.00 H HETATM 16 HD2 9XQ A 1 1.360 -8.583 -2.549 1.00 0.00 H HETATM 17 HH12 9XQ A 1 5.405 -10.373 1.277 1.00 0.00 H HETATM 18 HH11 9XQ A 1 7.047 -10.591 2.042 1.00 0.00 H HETATM 19 HH21 9XQ A 1 8.585 -8.105 0.338 1.00 0.00 H HETATM 20 HE3 9XQ A 1 6.725 -7.693 -0.576 1.00 0.00 H HETATM 21 HH22 9XQ A 1 8.595 -9.439 1.566 1.00 0.00 H