HEADER SIGNALING PROTEIN, HYDROLASE/ANTIBIOTIC 12-AUG-10 3OE0 TITLE CRYSTAL STRUCTURE OF THE CXCR4 CHEMOKINE RECEPTOR IN COMPLEX WITH A TITLE 2 CYCLIC PEPTIDE ANTAGONIST CVX15 COMPND MOL_ID: 1; COMPND 2 MOLECULE: C-X-C CHEMOKINE RECEPTOR TYPE 4, LYSOZYME CHIMERA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CXCR4 RESIDUES 2-228, LYSOZYME RESIDUES 1002-1161, CXCR4 COMPND 5 RESIDUES 231-319; COMPND 6 SYNONYM: CXC-R4, CXCR-4, STROMAL CELL-DERIVED FACTOR 1 RECEPTOR, SDF- COMPND 7 1 RECEPTOR, FUSIN, LEUKOCYTE-DERIVED SEVEN TRANSMEMBRANE DOMAIN COMPND 8 RECEPTOR, LESTR, LCR1, FB22, NPYRL, HM89, LYSIS PROTEIN, MURAMIDASE, COMPND 9 ENDOLYSIN; COMPND 10 EC: 3.2.1.17; COMPND 11 ENGINEERED: YES; COMPND 12 MUTATION: YES; COMPND 13 MOL_ID: 2; COMPND 14 MOLECULE: POLYPHEMUSIN ANALOG, CXC CHEMOKINE RECEPTOR ANTAGONIST; COMPND 15 CHAIN: I; COMPND 16 ENGINEERED: YES; COMPND 17 OTHER_DETAILS: CYCLIC PEPTIDE CVX15 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS, ENTEROBACTERIA PHAGE T4; SOURCE 3 ORGANISM_TAXID: 9606, 10665; SOURCE 4 GENE: CXCR4, CXCR4_HUMAN, E; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: SF9; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: BACMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PFASTBAC; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: SYNTHETIC ANALOG AND DERIVATIVE OF POLYPHEMUSIN FROM SOURCE 13 LIMULUS POLYPHEMUS (HORSESHOE CRAB) KEYWDS STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, ACCELERATED KEYWDS 2 TECHNOLOGIES CENTER FOR GENE TO 3D STRUCTURE, ATCG3D, 7TM, G KEYWDS 3 PROTEIN-COUPLED RECEPTOR, GPCR, SIGNAL TRANSDUCTION, HYDROLASE, KEYWDS 4 CANCER, HIV-1 CO-RECEPTOR, CHEMOKINE, CXCL12, CHIMERA, T4L FUSION, KEYWDS 5 MEMBRANE PROTEIN, TRANSMEMBRANE, ANTIMICROBIAL, ANTIBIOTIC, KEYWDS 6 POLYPHEMUSIN, SIGNALING PROTEIN, HYDROLASE-ANTIBIOTIC COMPLEX, PSI- KEYWDS 7 BIOLOGY, GPCR NETWORK EXPDTA X-RAY DIFFRACTION AUTHOR B.WU,C.D.MOL,G.W.HAN,V.KATRITCH,E.Y.T.CHIEN,W.LIU,V.CHEREZOV, AUTHOR 2 R.C.STEVENS,ACCELERATED TECHNOLOGIES CENTER FOR GENE TO 3D STRUCTURE AUTHOR 3 (ATCG3D),GPCR NETWORK (GPCR) REVDAT 8 15-NOV-23 3OE0 1 DBREF LINK ATOM REVDAT 7 06-OCT-21 3OE0 1 SEQADV LINK REVDAT 6 26-JUL-17 3OE0 1 SOURCE REMARK REVDAT 5 02-MAY-12 3OE0 1 REMARK VERSN REVDAT 4 16-FEB-11 3OE0 1 HEADER REVDAT 3 05-JAN-11 3OE0 1 JRNL REVDAT 2 01-DEC-10 3OE0 1 COMPND LINK REMARK REVDAT 1 27-OCT-10 3OE0 0 JRNL AUTH B.WU,E.Y.CHIEN,C.D.MOL,G.FENALTI,W.LIU,V.KATRITCH,R.ABAGYAN, JRNL AUTH 2 A.BROOUN,P.WELLS,F.C.BI,D.J.HAMEL,P.KUHN,T.M.HANDEL, JRNL AUTH 3 V.CHEREZOV,R.C.STEVENS JRNL TITL STRUCTURES OF THE CXCR4 CHEMOKINE GPCR WITH SMALL-MOLECULE JRNL TITL 2 AND CYCLIC PEPTIDE ANTAGONISTS. JRNL REF SCIENCE V. 330 1066 2010 JRNL REFN ISSN 0036-8075 JRNL PMID 20929726 JRNL DOI 10.1126/SCIENCE.1194396 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0088 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 16707 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) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 898 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) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 961 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.60 REMARK 3 BIN R VALUE (WORKING SET) : 0.3400 REMARK 3 BIN FREE R VALUE SET COUNT : 40 REMARK 3 BIN FREE R VALUE : 0.3970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3634 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 6 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.10000 REMARK 3 B22 (A**2) : -0.41000 REMARK 3 B33 (A**2) : 0.41000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.20000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.839 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.374 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.309 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 34.246 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3728 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2530 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5053 ; 1.101 ; 1.956 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6125 ; 0.855 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 441 ; 5.801 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 162 ;37.366 ;22.840 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 625 ;18.646 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;15.924 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 572 ; 0.060 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4046 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 822 ; 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): 2232 ; 0.385 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 901 ; 0.045 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3608 ; 0.733 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1496 ; 0.802 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1445 ; 1.419 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 25 A 228 REMARK 3 ORIGIN FOR THE GROUP (A): 56.8558 15.0034 6.2863 REMARK 3 T TENSOR REMARK 3 T11: 0.0526 T22: 0.1669 REMARK 3 T33: 0.2390 T12: -0.0106 REMARK 3 T13: 0.0657 T23: -0.0696 REMARK 3 L TENSOR REMARK 3 L11: 0.1326 L22: 1.6844 REMARK 3 L33: 1.1636 L12: 0.2962 REMARK 3 L13: 0.2334 L23: -0.2676 REMARK 3 S TENSOR REMARK 3 S11: -0.0594 S12: 0.0472 S13: -0.0348 REMARK 3 S21: -0.1450 S22: 0.1410 S23: -0.2135 REMARK 3 S31: -0.0219 S32: 0.1337 S33: -0.0817 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1002 A 1161 REMARK 3 ORIGIN FOR THE GROUP (A): 35.2422 -20.8302 24.5296 REMARK 3 T TENSOR REMARK 3 T11: 0.1686 T22: 0.0892 REMARK 3 T33: 0.1050 T12: -0.0329 REMARK 3 T13: -0.0135 T23: 0.0187 REMARK 3 L TENSOR REMARK 3 L11: 4.4070 L22: 0.3599 REMARK 3 L33: 1.9082 L12: 0.9320 REMARK 3 L13: 0.7447 L23: -0.3647 REMARK 3 S TENSOR REMARK 3 S11: -0.2832 S12: 0.0474 S13: -0.0242 REMARK 3 S21: -0.1104 S22: 0.0112 S23: -0.0591 REMARK 3 S31: 0.0904 S32: 0.0806 S33: 0.2720 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 231 A 303 REMARK 3 ORIGIN FOR THE GROUP (A): 50.1136 16.3673 15.7284 REMARK 3 T TENSOR REMARK 3 T11: 0.1509 T22: 0.1712 REMARK 3 T33: 0.1511 T12: -0.0758 REMARK 3 T13: 0.0310 T23: -0.0263 REMARK 3 L TENSOR REMARK 3 L11: 0.4506 L22: 3.7115 REMARK 3 L33: 1.0419 L12: -0.6918 REMARK 3 L13: -0.4711 L23: 0.5601 REMARK 3 S TENSOR REMARK 3 S11: 0.0483 S12: -0.0562 S13: 0.0183 REMARK 3 S21: 0.4368 S22: -0.1400 S23: 0.0068 REMARK 3 S31: 0.0942 S32: -0.0059 S33: 0.0917 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3OE0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-OCT-10. REMARK 100 THE DEPOSITION ID IS D_1000060996. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUN-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 14 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0330 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17656 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.63000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.500 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: LIPIDIC CUBIC PHASE MADE OF MONOOLEIN REMARK 280 AND CHOLESTEROL, 25% PEG400, 0.3M POTASSIUM SODIUM TARTRATE, 0.1 REMARK 280 M TRIS PH 7.0, LIPIDIC CUBIC PHASE, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Z 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 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 41.04000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 72.43000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 41.04000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 72.43000 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, I 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 BIOMT1 2 -1.000000 0.000000 0.000000 82.08000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE POLYPHEMUSIN ANALOG, CXC CHEMOKINE RECEPTOR ANTAGONIST IS REMARK 400 OLIGOPEPTIDE, A MEMBER OF ANTAGONIST CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: POLYPHEMUSIN ANALOG, CXC CHEMOKINE RECEPTOR ANTAGONIST REMARK 400 CHAIN: I REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 A -9 REMARK 465 TYR A -8 REMARK 465 LYS A -7 REMARK 465 ASP A -6 REMARK 465 ASP A -5 REMARK 465 ASP A -4 REMARK 465 ASP A -3 REMARK 465 ALA A -2 REMARK 465 GLY A -1 REMARK 465 ALA A 0 REMARK 465 PRO A 1 REMARK 465 GLU A 2 REMARK 465 GLY A 3 REMARK 465 ILE A 4 REMARK 465 SER A 5 REMARK 465 ILE A 6 REMARK 465 TYR A 7 REMARK 465 THR A 8 REMARK 465 SER A 9 REMARK 465 ASP A 10 REMARK 465 ASN A 11 REMARK 465 TYR A 12 REMARK 465 THR A 13 REMARK 465 GLU A 14 REMARK 465 GLU A 15 REMARK 465 MET A 16 REMARK 465 GLY A 17 REMARK 465 SER A 18 REMARK 465 GLY A 19 REMARK 465 ASP A 20 REMARK 465 TYR A 21 REMARK 465 ASP A 22 REMARK 465 SER A 23 REMARK 465 MET A 24 REMARK 465 LYS A 67 REMARK 465 LYS A 68 REMARK 465 LEU A 69 REMARK 465 ARG A 70 REMARK 465 SER A 1200 REMARK 465 GLY A 1201 REMARK 465 SER A 1202 REMARK 465 PHE A 304 REMARK 465 LEU A 305 REMARK 465 GLY A 306 REMARK 465 ALA A 307 REMARK 465 LYS A 308 REMARK 465 PHE A 309 REMARK 465 LYS A 310 REMARK 465 THR A 311 REMARK 465 SER A 312 REMARK 465 ALA A 313 REMARK 465 GLN A 314 REMARK 465 HIS A 315 REMARK 465 ALA A 316 REMARK 465 LEU A 317 REMARK 465 THR A 318 REMARK 465 SER A 319 REMARK 465 GLY A 320 REMARK 465 ARG A 321 REMARK 465 PRO A 322 REMARK 465 LEU A 323 REMARK 465 GLU A 324 REMARK 465 VAL A 325 REMARK 465 LEU A 326 REMARK 465 PHE A 327 REMARK 465 GLN A 328 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 GLN A 233 CG CD OE1 NE2 REMARK 470 LYS A 234 CG CD CE NZ 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 I 2 CA - C - N ANGL. DEV. = 17.3 DEGREES REMARK 500 ARG I 2 O - C - N ANGL. DEV. = -16.3 DEGREES REMARK 500 ARG I 11 CA - C - N ANGL. DEV. = 13.5 DEGREES REMARK 500 ARG I 11 O - C - N ANGL. DEV. = -13.9 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 TYR A 65 -165.19 -111.28 REMARK 500 ALA A 100 -74.07 -115.86 REMARK 500 VAL A 160 -63.58 -124.08 REMARK 500 ARG A1080 40.34 -109.31 REMARK 500 GLN A 233 77.07 42.60 REMARK 500 LYS A 234 48.31 -142.01 REMARK 500 GLN A 272 23.36 -148.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 CIR I 12 CYS I 13 149.89 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 CHAIN I OF POLYPHEMUSIN ANALOG, REMARK 800 CXC CHEMOKINE RECEPTOR ANTAGONIST REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: ATCG3D_11 RELATED DB: TARGETDB REMARK 900 RELATED ID: 3ODU RELATED DB: PDB REMARK 900 SAME PROTEIN AT 2.5 A IN P21 SPACEGROUP REMARK 900 RELATED ID: 3OE6 RELATED DB: PDB REMARK 900 SAME PROTEIN IN I222 SPACEGROUP REMARK 900 RELATED ID: 3OE8 RELATED DB: PDB REMARK 900 SAME PROTEIN IN P1 SPACEGROUP WITH 3 MOLECULES PER ASYMMETRIC UNIT REMARK 900 RELATED ID: 3OE9 RELATED DB: PDB REMARK 900 SAME PROTEIN IN P1 SPACEGROUP WITH 2 MOLECULES PER ASYMMETRIC UNIT REMARK 900 RELATED ID: GPCR-34 RELATED DB: TARGETTRACK REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE PROTEIN IS A FUSION PROTEIN WITH RESIDUES ASN1002-TYR1161 OF T4 REMARK 999 LYSOZYME INSERTED BETWEEN HIS228 AND GLY231 OF CXCR4, AS INDICATED REMARK 999 AS CXCR4-3 IN THE PUBLICATION. THE SMALL CYCLIC PEPTIDE NAMED CVX15 REMARK 999 IS CXC CHEMOKINE RECEPTOR (CXCR)4 ANTAGONIST, AS WELL AS ANALOG OF REMARK 999 POLYPHEMUSIN FROM LIMULUS POLYPHEMUS (HORSESHOE CRAB). PART OF THE REMARK 999 SEQUENCE OF THE SMALL PEPTIDE HAS SIMILARITY TO UNITPROT ENTRY REMARK 999 P14215 WITH SEQUENCE RRWCFRVCYRGFCYRKCR DBREF 3OE0 A 2 228 UNP P61073 CXCR4_HUMAN 2 228 DBREF 3OE0 A 1002 1161 UNP P00720 LYS_BPT4 1002 1161 DBREF 3OE0 A 231 319 UNP P61073 CXCR4_HUMAN 231 319 DBREF 3OE0 I 1 16 PDB 3OE0 3OE0 1 16 SEQADV 3OE0 ASP A -9 UNP P61073 EXPRESSION TAG SEQADV 3OE0 TYR A -8 UNP P61073 EXPRESSION TAG SEQADV 3OE0 LYS A -7 UNP P61073 EXPRESSION TAG SEQADV 3OE0 ASP A -6 UNP P61073 EXPRESSION TAG SEQADV 3OE0 ASP A -5 UNP P61073 EXPRESSION TAG SEQADV 3OE0 ASP A -4 UNP P61073 EXPRESSION TAG SEQADV 3OE0 ASP A -3 UNP P61073 EXPRESSION TAG SEQADV 3OE0 ALA A -2 UNP P61073 EXPRESSION TAG SEQADV 3OE0 GLY A -1 UNP P61073 EXPRESSION TAG SEQADV 3OE0 ALA A 0 UNP P61073 EXPRESSION TAG SEQADV 3OE0 PRO A 1 UNP P61073 EXPRESSION TAG SEQADV 3OE0 TRP A 125 UNP P61073 LEU 125 ENGINEERED MUTATION SEQADV 3OE0 THR A 1054 UNP P00720 CYS 1054 ENGINEERED MUTATION SEQADV 3OE0 ALA A 1097 UNP P00720 CYS 1097 ENGINEERED MUTATION SEQADV 3OE0 SER A 1200 UNP P61073 LINKER SEQADV 3OE0 GLY A 1201 UNP P61073 LINKER SEQADV 3OE0 SER A 1202 UNP P61073 LINKER SEQADV 3OE0 PRO A 240 UNP P61073 THR 240 ENGINEERED MUTATION SEQADV 3OE0 GLY A 320 UNP P61073 EXPRESSION TAG SEQADV 3OE0 ARG A 321 UNP P61073 EXPRESSION TAG SEQADV 3OE0 PRO A 322 UNP P61073 EXPRESSION TAG SEQADV 3OE0 LEU A 323 UNP P61073 EXPRESSION TAG SEQADV 3OE0 GLU A 324 UNP P61073 EXPRESSION TAG SEQADV 3OE0 VAL A 325 UNP P61073 EXPRESSION TAG SEQADV 3OE0 LEU A 326 UNP P61073 EXPRESSION TAG SEQADV 3OE0 PHE A 327 UNP P61073 EXPRESSION TAG SEQADV 3OE0 GLN A 328 UNP P61073 EXPRESSION TAG SEQRES 1 A 499 ASP TYR LYS ASP ASP ASP ASP ALA GLY ALA PRO GLU GLY SEQRES 2 A 499 ILE SER ILE TYR THR SER ASP ASN TYR THR GLU GLU MET SEQRES 3 A 499 GLY SER GLY ASP TYR ASP SER MET LYS GLU PRO CYS PHE SEQRES 4 A 499 ARG GLU GLU ASN ALA ASN PHE ASN LYS ILE PHE LEU PRO SEQRES 5 A 499 THR ILE TYR SER ILE ILE PHE LEU THR GLY ILE VAL GLY SEQRES 6 A 499 ASN GLY LEU VAL ILE LEU VAL MET GLY TYR GLN LYS LYS SEQRES 7 A 499 LEU ARG SER MET THR ASP LYS TYR ARG LEU HIS LEU SER SEQRES 8 A 499 VAL ALA ASP LEU LEU PHE VAL ILE THR LEU PRO PHE TRP SEQRES 9 A 499 ALA VAL ASP ALA VAL ALA ASN TRP TYR PHE GLY ASN PHE SEQRES 10 A 499 LEU CYS LYS ALA VAL HIS VAL ILE TYR THR VAL ASN LEU SEQRES 11 A 499 TYR SER SER VAL TRP ILE LEU ALA PHE ILE SER LEU ASP SEQRES 12 A 499 ARG TYR LEU ALA ILE VAL HIS ALA THR ASN SER GLN ARG SEQRES 13 A 499 PRO ARG LYS LEU LEU ALA GLU LYS VAL VAL TYR VAL GLY SEQRES 14 A 499 VAL TRP ILE PRO ALA LEU LEU LEU THR ILE PRO ASP PHE SEQRES 15 A 499 ILE PHE ALA ASN VAL SER GLU ALA ASP ASP ARG TYR ILE SEQRES 16 A 499 CYS ASP ARG PHE TYR PRO ASN ASP LEU TRP VAL VAL VAL SEQRES 17 A 499 PHE GLN PHE GLN HIS ILE MET VAL GLY LEU ILE LEU PRO SEQRES 18 A 499 GLY ILE VAL ILE LEU SER CYS TYR CYS ILE ILE ILE SER SEQRES 19 A 499 LYS LEU SER HIS ASN ILE PHE GLU MET LEU ARG ILE ASP SEQRES 20 A 499 GLU GLY LEU ARG LEU LYS ILE TYR LYS ASP THR GLU GLY SEQRES 21 A 499 TYR TYR THR ILE GLY ILE GLY HIS LEU LEU THR LYS SER SEQRES 22 A 499 PRO SER LEU ASN ALA ALA LYS SER GLU LEU ASP LYS ALA SEQRES 23 A 499 ILE GLY ARG ASN THR ASN GLY VAL ILE THR LYS ASP GLU SEQRES 24 A 499 ALA GLU LYS LEU PHE ASN GLN ASP VAL ASP ALA ALA VAL SEQRES 25 A 499 ARG GLY ILE LEU ARG ASN ALA LYS LEU LYS PRO VAL TYR SEQRES 26 A 499 ASP SER LEU ASP ALA VAL ARG ARG ALA ALA LEU ILE ASN SEQRES 27 A 499 MET VAL PHE GLN MET GLY GLU THR GLY VAL ALA GLY PHE SEQRES 28 A 499 THR ASN SER LEU ARG MET LEU GLN GLN LYS ARG TRP ASP SEQRES 29 A 499 GLU ALA ALA VAL ASN LEU ALA LYS SER ARG TRP TYR ASN SEQRES 30 A 499 GLN THR PRO ASN ARG ALA LYS ARG VAL ILE THR THR PHE SEQRES 31 A 499 ARG THR GLY THR TRP ASP ALA TYR SER GLY SER GLY HIS SEQRES 32 A 499 GLN LYS ARG LYS ALA LEU LYS PRO THR VAL ILE LEU ILE SEQRES 33 A 499 LEU ALA PHE PHE ALA CYS TRP LEU PRO TYR TYR ILE GLY SEQRES 34 A 499 ILE SER ILE ASP SER PHE ILE LEU LEU GLU ILE ILE LYS SEQRES 35 A 499 GLN GLY CYS GLU PHE GLU ASN THR VAL HIS LYS TRP ILE SEQRES 36 A 499 SER ILE THR GLU ALA LEU ALA PHE PHE HIS CYS CYS LEU SEQRES 37 A 499 ASN PRO ILE LEU TYR ALA PHE LEU GLY ALA LYS PHE LYS SEQRES 38 A 499 THR SER ALA GLN HIS ALA LEU THR SER GLY ARG PRO LEU SEQRES 39 A 499 GLU VAL LEU PHE GLN SEQRES 1 I 16 ARG ARG ALN CYS TYR GLN LYS DPR PRO TYR ARG CIR CYS SEQRES 2 I 16 ARG GLY DPR MODRES 3OE0 ALN I 3 ALA NAPHTHALEN-2-YL-3-ALANINE MODRES 3OE0 CIR I 12 ARG CITRULLINE HET ALN I 3 15 HET DPR I 8 7 HET CIR I 12 11 HET DPR I 16 8 HETNAM ALN NAPHTHALEN-2-YL-3-ALANINE HETNAM DPR D-PROLINE HETNAM CIR CITRULLINE FORMUL 2 ALN C13 H13 N O2 FORMUL 2 DPR 2(C5 H9 N O2) FORMUL 2 CIR C6 H13 N3 O3 FORMUL 3 HOH *6(H2 O) HELIX 1 1 ASN A 33 ILE A 39 1 7 HELIX 2 2 ILE A 39 MET A 63 1 25 HELIX 3 3 SER A 71 ILE A 89 1 19 HELIX 4 4 THR A 90 ALA A 100 1 11 HELIX 5 5 PHE A 104 HIS A 140 1 37 HELIX 6 6 ALA A 141 ASN A 143 5 3 HELIX 7 7 SER A 144 LYS A 154 1 11 HELIX 8 8 LYS A 154 VAL A 160 1 7 HELIX 9 9 VAL A 160 THR A 168 1 9 HELIX 10 10 THR A 168 PHE A 174 1 7 HELIX 11 11 ASN A 192 LEU A 208 1 17 HELIX 12 12 LEU A 208 GLU A 1011 1 31 HELIX 13 13 SER A 1038 GLY A 1051 1 14 HELIX 14 14 THR A 1059 ARG A 1080 1 22 HELIX 15 15 LYS A 1083 LEU A 1091 1 9 HELIX 16 16 ASP A 1092 GLY A 1113 1 22 HELIX 17 17 PHE A 1114 GLN A 1123 1 10 HELIX 18 18 ARG A 1125 LYS A 1135 1 11 HELIX 19 19 SER A 1136 THR A 1142 1 7 HELIX 20 20 THR A 1142 GLY A 1156 1 15 HELIX 21 21 LEU A 238 LEU A 267 1 30 HELIX 22 22 GLN A 272 PHE A 292 1 21 HELIX 23 23 PHE A 293 TYR A 302 1 10 SHEET 1 A 3 ALA A 175 GLU A 179 0 SHEET 2 A 3 TYR A 184 TYR A 190 -1 O ILE A 185 N SER A 178 SHEET 3 A 3 CYS I 4 TYR I 5 1 O CYS I 4 N ARG A 188 SHEET 1 B 3 LEU A1013 LYS A1019 0 SHEET 2 B 3 TYR A1025 ILE A1029 -1 O GLY A1028 N ARG A1014 SHEET 3 B 3 HIS A1031 THR A1034 -1 O LEU A1033 N TYR A1025 SSBOND 1 CYS A 28 CYS A 274 1555 1555 2.04 SSBOND 2 CYS A 109 CYS A 186 1555 1555 2.05 SSBOND 3 CYS I 4 CYS I 13 1555 1555 2.06 LINK C HIS A 228 N ASN A1002 1555 1555 1.33 LINK C ARG I 2 N ALN I 3 1555 1555 1.34 LINK C ALN I 3 N CYS I 4 1555 1555 1.33 LINK C LYS I 7 N DPR I 8 1555 1555 1.35 LINK C DPR I 8 N PRO I 9 1555 1555 1.34 LINK C ARG I 11 N CIR I 12 1555 1555 1.34 LINK C CIR I 12 N CYS I 13 1555 1555 1.33 LINK C GLY I 15 N DPR I 16 1555 1555 1.34 SITE 1 AC1 23 HIS A 113 TYR A 116 THR A 117 ASP A 171 SITE 2 AC1 23 ASP A 187 ARG A 188 PHE A 189 TYR A 190 SITE 3 AC1 23 PRO A 191 ASP A 193 VAL A 196 PHE A 199 SITE 4 AC1 23 GLN A 200 ASP A 262 LEU A 266 GLU A 277 SITE 5 AC1 23 HIS A 281 ILE A 284 SER A 285 GLU A 288 SITE 6 AC1 23 HOH I1601 HOH I1602 HOH I1604 CRYST1 82.080 144.860 73.990 90.00 104.54 90.00 C 1 2 1 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 0.012183 0.000000 0.003160 0.00000 SCALE2 0.000000 0.006903 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013963 0.00000