HEADER SIGNALING PROTEIN, HYDROLASE 12-AUG-10 3OE6 TITLE CRYSTAL STRUCTURE OF THE CXCR4 CHEMOKINE RECEPTOR IN COMPLEX WITH A TITLE 2 SMALL MOLECULE ANTAGONIST IT1T IN I222 SPACEGROUP 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 231-325; 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 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 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, SDF1, ISOTHIOUREA, KEYWDS 5 IT1T, CHIMERA, T4L FUSION, MEMBRANE PROTEIN, TRANSMEMBRANE, KEYWDS 6 SINGNALING PROTEIN, PSI-BIOLOGY, GPCR NETWORK, SIGNALING PROTEIN 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 6 06-OCT-21 3OE6 1 REMARK SEQADV REVDAT 5 26-JUL-17 3OE6 1 SOURCE REMARK REVDAT 4 02-MAY-12 3OE6 1 REMARK VERSN REVDAT 3 16-FEB-11 3OE6 1 HEADER REVDAT 2 05-JAN-11 3OE6 1 JRNL REVDAT 1 27-OCT-10 3OE6 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. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.8.0 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 8310 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) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.306 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 406 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 3.20 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 3.58 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2289 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2434 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2172 REMARK 3 BIN R VALUE (WORKING SET) : 0.2415 REMARK 3 BIN FREE R VALUE : 0.2797 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.11 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 117 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3356 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 79 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 89.11 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.48050 REMARK 3 B22 (A**2) : 5.02820 REMARK 3 B33 (A**2) : -3.54760 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.578 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.847 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.747 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 3521 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4767 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1170 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 61 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 501 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 3448 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 463 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 3940 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.31 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.92 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 22.48 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|35 - A|226 } REMARK 3 ORIGIN FOR THE GROUP (A): 16.6490 31.6020 57.3607 REMARK 3 T TENSOR REMARK 3 T11: -0.1656 T22: -0.1593 REMARK 3 T33: -0.0392 T12: 0.0343 REMARK 3 T13: -0.0383 T23: 0.0039 REMARK 3 L TENSOR REMARK 3 L11: 1.7894 L22: 2.3820 REMARK 3 L33: 2.7213 L12: -0.2014 REMARK 3 L13: -0.0230 L23: 0.7673 REMARK 3 S TENSOR REMARK 3 S11: 0.0141 S12: 0.0783 S13: 0.2435 REMARK 3 S21: 0.0109 S22: -0.0029 S23: -0.2000 REMARK 3 S31: 0.2532 S32: 0.1668 S33: -0.0112 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { A|1010 - A|1159 } REMARK 3 ORIGIN FOR THE GROUP (A): 1.4948 23.5205 11.2511 REMARK 3 T TENSOR REMARK 3 T11: -0.0243 T22: 0.2227 REMARK 3 T33: -0.3040 T12: 0.1520 REMARK 3 T13: 0.0225 T23: 0.0184 REMARK 3 L TENSOR REMARK 3 L11: 0.0000 L22: 0.8159 REMARK 3 L33: 2.9429 L12: 0.2535 REMARK 3 L13: -0.7642 L23: 0.0777 REMARK 3 S TENSOR REMARK 3 S11: -0.0079 S12: -0.0205 S13: 0.0195 REMARK 3 S21: 0.0870 S22: 0.2047 S23: 0.0639 REMARK 3 S31: 0.4021 S32: 0.0755 S33: -0.1969 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { A|235 - A|312 } REMARK 3 ORIGIN FOR THE GROUP (A): 10.1585 19.8890 60.4589 REMARK 3 T TENSOR REMARK 3 T11: -0.0082 T22: -0.0729 REMARK 3 T33: 0.0056 T12: -0.0193 REMARK 3 T13: -0.0115 T23: 0.0074 REMARK 3 L TENSOR REMARK 3 L11: 1.5458 L22: 0.9685 REMARK 3 L33: 0.0000 L12: -0.4452 REMARK 3 L13: 0.3227 L23: 0.5188 REMARK 3 S TENSOR REMARK 3 S11: 0.0855 S12: -0.1813 S13: -0.2110 REMARK 3 S21: -0.0025 S22: -0.0681 S23: -0.0897 REMARK 3 S31: 0.1624 S32: -0.0264 S33: -0.0174 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3OE6 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_1000061002. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 4 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10233 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 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 (%) : 94.4 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.13600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.67000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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 (%): 57.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: LIPIDIC CUBIC PHASE MADE OF MONOOLEIN REMARK 280 AND CHOLESTEROL, 20-26% PEG400, 0.3M SODIUM MALONATE, 5MM NICKEL REMARK 280 CHLORIDE, 0.1M SODIUM CITRATE PH 5.0-5.5, LIPIDIC CUBIC PHASE, REMARK 280 TEMPERATURE 293K, PH 5.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 35.56050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.35550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 120.29600 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 35.56050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.35550 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 120.29600 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 35.56050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 39.35550 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 120.29600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 35.56050 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 39.35550 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 120.29600 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: 2640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 47890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 78.71100 REMARK 350 BIOMT3 2 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 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 25 REMARK 465 GLU A 26 REMARK 465 PRO A 27 REMARK 465 CYS A 28 REMARK 465 PHE A 29 REMARK 465 ARG A 30 REMARK 465 GLU A 31 REMARK 465 GLU A 32 REMARK 465 ASN A 33 REMARK 465 ALA A 34 REMARK 465 SER A 227 REMARK 465 HIS A 228 REMARK 465 SER A 229 REMARK 465 GLY A 900 REMARK 465 SER A 901 REMARK 465 ASN A 1002 REMARK 465 ILE A 1003 REMARK 465 PHE A 1004 REMARK 465 GLU A 1005 REMARK 465 MET A 1006 REMARK 465 LEU A 1007 REMARK 465 ARG A 1008 REMARK 465 ILE A 1009 REMARK 465 THR A 1115 REMARK 465 ASN A 1116 REMARK 465 ALA A 1160 REMARK 465 TYR A 1161 REMARK 465 GLY A 1200 REMARK 465 SER A 1201 REMARK 465 LYS A 230 REMARK 465 GLY A 231 REMARK 465 HIS A 232 REMARK 465 GLN A 233 REMARK 465 LYS A 234 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 VAL A 320 REMARK 465 SER A 321 REMARK 465 ARG A 322 REMARK 465 GLY A 323 REMARK 465 SER A 324 REMARK 465 SER A 325 REMARK 465 GLY A 326 REMARK 465 ARG A 327 REMARK 465 PRO A 328 REMARK 465 LEU A 329 REMARK 465 GLU A 330 REMARK 465 VAL A 331 REMARK 465 LEU A 332 REMARK 465 PHE A 333 REMARK 465 GLN A 334 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 ASP A 181 CG OD1 OD2 REMARK 470 THR A1059 OG1 CG2 REMARK 470 ASP A1092 CG OD1 OD2 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 O LYS A 38 CG PRO A 42 2.15 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 ALA A 98 CB - CA - C ANGL. DEV. = 9.9 DEGREES REMARK 500 ALA A 100 N - CA - CB ANGL. DEV. = -9.9 DEGREES REMARK 500 ASN A 101 N - CA - CB ANGL. DEV. = 12.3 DEGREES REMARK 500 PRO A 147 C - N - CD ANGL. DEV. = -14.4 DEGREES REMARK 500 LYS A1083 CB - CA - C ANGL. DEV. = 14.5 DEGREES REMARK 500 ASP A1092 CB - CA - C ANGL. DEV. = -17.1 DEGREES REMARK 500 ALA A1093 CB - CA - C ANGL. DEV. = -11.0 DEGREES REMARK 500 ALA A1093 N - CA - C ANGL. DEV. = 17.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 OLC A 1600 REMARK 610 OLC A 1601 REMARK 610 OLC A 1602 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ITD A 1500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OLC A 1600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OLC A 1601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OLC A 1602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1603 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: 3OE0 RELATED DB: PDB REMARK 900 SAME PROTEIN IN COMPLEX WITH A CYCLIC PEPTIDE CVX15 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 SER229 AND LYS230 OF CXCR4, AS INDICATED REMARK 999 AS CXCR4-1 IN THE PUBLICATION. DBREF 3OE6 A 2 229 UNP P61073 CXCR4_HUMAN 2 229 DBREF 3OE6 A 1002 1161 UNP P00720 LYS_BPT4 1002 1161 DBREF 3OE6 A 230 325 UNP P61073 CXCR4_HUMAN 230 325 SEQADV 3OE6 ASP A -9 UNP P61073 EXPRESSION TAG SEQADV 3OE6 TYR A -8 UNP P61073 EXPRESSION TAG SEQADV 3OE6 LYS A -7 UNP P61073 EXPRESSION TAG SEQADV 3OE6 ASP A -6 UNP P61073 EXPRESSION TAG SEQADV 3OE6 ASP A -5 UNP P61073 EXPRESSION TAG SEQADV 3OE6 ASP A -4 UNP P61073 EXPRESSION TAG SEQADV 3OE6 ASP A -3 UNP P61073 EXPRESSION TAG SEQADV 3OE6 ALA A -2 UNP P61073 EXPRESSION TAG SEQADV 3OE6 GLY A -1 UNP P61073 EXPRESSION TAG SEQADV 3OE6 ALA A 0 UNP P61073 EXPRESSION TAG SEQADV 3OE6 PRO A 1 UNP P61073 EXPRESSION TAG SEQADV 3OE6 TRP A 125 UNP P61073 LEU 125 ENGINEERED MUTATION SEQADV 3OE6 GLY A 900 UNP P61073 LINKER SEQADV 3OE6 SER A 901 UNP P61073 LINKER SEQADV 3OE6 GLY A 1200 UNP P61073 LINKER SEQADV 3OE6 SER A 1201 UNP P61073 LINKER SEQADV 3OE6 THR A 1054 UNP P00720 CYS 1054 ENGINEERED MUTATION SEQADV 3OE6 ALA A 1097 UNP P00720 CYS 1097 ENGINEERED MUTATION SEQADV 3OE6 GLY A 326 UNP P61073 EXPRESSION TAG SEQADV 3OE6 ARG A 327 UNP P61073 EXPRESSION TAG SEQADV 3OE6 PRO A 328 UNP P61073 EXPRESSION TAG SEQADV 3OE6 LEU A 329 UNP P61073 EXPRESSION TAG SEQADV 3OE6 GLU A 330 UNP P61073 EXPRESSION TAG SEQADV 3OE6 VAL A 331 UNP P61073 EXPRESSION TAG SEQADV 3OE6 LEU A 332 UNP P61073 EXPRESSION TAG SEQADV 3OE6 PHE A 333 UNP P61073 EXPRESSION TAG SEQADV 3OE6 GLN A 334 UNP P61073 EXPRESSION TAG SEQRES 1 A 508 ASP TYR LYS ASP ASP ASP ASP ALA GLY ALA PRO GLU GLY SEQRES 2 A 508 ILE SER ILE TYR THR SER ASP ASN TYR THR GLU GLU MET SEQRES 3 A 508 GLY SER GLY ASP TYR ASP SER MET LYS GLU PRO CYS PHE SEQRES 4 A 508 ARG GLU GLU ASN ALA ASN PHE ASN LYS ILE PHE LEU PRO SEQRES 5 A 508 THR ILE TYR SER ILE ILE PHE LEU THR GLY ILE VAL GLY SEQRES 6 A 508 ASN GLY LEU VAL ILE LEU VAL MET GLY TYR GLN LYS LYS SEQRES 7 A 508 LEU ARG SER MET THR ASP LYS TYR ARG LEU HIS LEU SER SEQRES 8 A 508 VAL ALA ASP LEU LEU PHE VAL ILE THR LEU PRO PHE TRP SEQRES 9 A 508 ALA VAL ASP ALA VAL ALA ASN TRP TYR PHE GLY ASN PHE SEQRES 10 A 508 LEU CYS LYS ALA VAL HIS VAL ILE TYR THR VAL ASN LEU SEQRES 11 A 508 TYR SER SER VAL TRP ILE LEU ALA PHE ILE SER LEU ASP SEQRES 12 A 508 ARG TYR LEU ALA ILE VAL HIS ALA THR ASN SER GLN ARG SEQRES 13 A 508 PRO ARG LYS LEU LEU ALA GLU LYS VAL VAL TYR VAL GLY SEQRES 14 A 508 VAL TRP ILE PRO ALA LEU LEU LEU THR ILE PRO ASP PHE SEQRES 15 A 508 ILE PHE ALA ASN VAL SER GLU ALA ASP ASP ARG TYR ILE SEQRES 16 A 508 CYS ASP ARG PHE TYR PRO ASN ASP LEU TRP VAL VAL VAL SEQRES 17 A 508 PHE GLN PHE GLN HIS ILE MET VAL GLY LEU ILE LEU PRO SEQRES 18 A 508 GLY ILE VAL ILE LEU SER CYS TYR CYS ILE ILE ILE SER SEQRES 19 A 508 LYS LEU SER HIS SER GLY SER ASN ILE PHE GLU MET LEU SEQRES 20 A 508 ARG ILE ASP GLU GLY LEU ARG LEU LYS ILE TYR LYS ASP SEQRES 21 A 508 THR GLU GLY TYR TYR THR ILE GLY ILE GLY HIS LEU LEU SEQRES 22 A 508 THR LYS SER PRO SER LEU ASN ALA ALA LYS SER GLU LEU SEQRES 23 A 508 ASP LYS ALA ILE GLY ARG ASN THR ASN GLY VAL ILE THR SEQRES 24 A 508 LYS ASP GLU ALA GLU LYS LEU PHE ASN GLN ASP VAL ASP SEQRES 25 A 508 ALA ALA VAL ARG GLY ILE LEU ARG ASN ALA LYS LEU LYS SEQRES 26 A 508 PRO VAL TYR ASP SER LEU ASP ALA VAL ARG ARG ALA ALA SEQRES 27 A 508 LEU ILE ASN MET VAL PHE GLN MET GLY GLU THR GLY VAL SEQRES 28 A 508 ALA GLY PHE THR ASN SER LEU ARG MET LEU GLN GLN LYS SEQRES 29 A 508 ARG TRP ASP GLU ALA ALA VAL ASN LEU ALA LYS SER ARG SEQRES 30 A 508 TRP TYR ASN GLN THR PRO ASN ARG ALA LYS ARG VAL ILE SEQRES 31 A 508 THR THR PHE ARG THR GLY THR TRP ASP ALA TYR GLY SER SEQRES 32 A 508 LYS GLY HIS GLN LYS ARG LYS ALA LEU LYS THR THR VAL SEQRES 33 A 508 ILE LEU ILE LEU ALA PHE PHE ALA CYS TRP LEU PRO TYR SEQRES 34 A 508 TYR ILE GLY ILE SER ILE ASP SER PHE ILE LEU LEU GLU SEQRES 35 A 508 ILE ILE LYS GLN GLY CYS GLU PHE GLU ASN THR VAL HIS SEQRES 36 A 508 LYS TRP ILE SER ILE THR GLU ALA LEU ALA PHE PHE HIS SEQRES 37 A 508 CYS CYS LEU ASN PRO ILE LEU TYR ALA PHE LEU GLY ALA SEQRES 38 A 508 LYS PHE LYS THR SER ALA GLN HIS ALA LEU THR SER VAL SEQRES 39 A 508 SER ARG GLY SER SER GLY ARG PRO LEU GLU VAL LEU PHE SEQRES 40 A 508 GLN HET ITD A1500 27 HET OLC A1600 15 HET OLC A1601 15 HET OLC A1602 16 HET GOL A1603 6 HETNAM ITD (6,6-DIMETHYL-5,6-DIHYDROIMIDAZO[2,1-B][1,3]THIAZOL-3- HETNAM 2 ITD YL)METHYL N,N'-DICYCLOHEXYLIMIDOTHIOCARBAMATE HETNAM OLC (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE HETNAM GOL GLYCEROL HETSYN OLC 1-OLEOYL-R-GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ITD C21 H34 N4 S2 FORMUL 3 OLC 3(C21 H40 O4) FORMUL 6 GOL C3 H8 O3 HELIX 1 1 PHE A 36 GLN A 66 1 31 HELIX 2 2 SER A 71 ILE A 89 1 19 HELIX 3 3 THR A 90 ALA A 100 1 11 HELIX 4 4 GLY A 105 HIS A 140 1 36 HELIX 5 5 SER A 144 LYS A 154 1 11 HELIX 6 6 LYS A 154 GLY A 159 1 6 HELIX 7 7 VAL A 160 LEU A 167 1 8 HELIX 8 8 THR A 168 PHE A 174 1 7 HELIX 9 9 ASP A 193 LEU A 208 1 16 HELIX 10 10 LEU A 208 LYS A 225 1 18 HELIX 11 11 SER A 1038 LEU A 1046 1 9 HELIX 12 12 THR A 1059 VAL A 1075 1 17 HELIX 13 13 LEU A 1084 LEU A 1091 1 8 HELIX 14 14 ASP A 1092 GLY A 1107 1 16 HELIX 15 15 GLY A 1110 PHE A 1114 5 5 HELIX 16 16 LEU A 1118 GLN A 1123 1 6 HELIX 17 17 ARG A 1125 ALA A 1134 1 10 HELIX 18 18 ARG A 1137 THR A 1142 1 6 HELIX 19 19 THR A 1142 THR A 1155 1 14 HELIX 20 20 ARG A 235 LEU A 267 1 33 HELIX 21 21 CYS A 274 TRP A 283 1 10 HELIX 22 22 ILE A 284 PHE A 292 1 9 HELIX 23 23 PHE A 293 CYS A 295 5 3 HELIX 24 24 CYS A 296 LEU A 301 1 6 SHEET 1 A 2 ALA A 175 ALA A 180 0 SHEET 2 A 2 ARG A 183 ARG A 188 -1 O ILE A 185 N SER A 178 SHEET 1 B 3 TYR A1018 LYS A1019 0 SHEET 2 B 3 TYR A1025 ILE A1027 -1 O THR A1026 N TYR A1018 SHEET 3 B 3 HIS A1031 THR A1034 -1 O HIS A1031 N ILE A1027 SSBOND 1 CYS A 109 CYS A 186 1555 1555 2.04 SITE 1 AC1 7 TRP A 94 ASP A 97 TYR A 116 ARG A 183 SITE 2 AC1 7 CYS A 186 ASP A 187 GLU A 288 SITE 1 AC2 8 LEU A 58 VAL A 59 VAL A 62 ILE A 269 SITE 2 AC2 8 ILE A 270 PRO A 299 TYR A 302 LEU A 305 SITE 1 AC3 4 VAL A 99 ALA A 100 TYR A 103 ILE A 223 SITE 1 AC4 5 LYS A 38 ILE A 39 PRO A 42 THR A 43 SITE 2 AC4 5 SER A 46 SITE 1 AC5 8 LEU A 120 SER A 123 VAL A 124 HIS A 203 SITE 2 AC5 8 GLY A 207 PHE A 248 TRP A 252 TYR A 256 CRYST1 71.121 78.711 240.592 90.00 90.00 90.00 I 2 2 2 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 0.014061 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012705 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004156 0.00000