HEADER LIPID TRANSPORT 24-OCT-06 2NNQ TITLE CRYSTAL STRUCTURE OF HUMAN ADIPOCYTE FATTY ACID BINDING PROTEIN IN TITLE 2 COMPLEX WITH ((2'-(5-ETHYL-3,4-DIPHENYL-1H-PYRAZOL-1-YL)-3- TITLE 3 BIPHENYLYL)OXY)ACETIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: FATTY ACID-BINDING PROTEIN, ADIPOCYTE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AFABP, ADIPOCYTE LIPID-BINDING PROTEIN, ALBP, A-FABP; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: FABP4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSPORT, LIPID-BINDING, LIPID TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR B.L.JACOBSON REVDAT 6 03-APR-24 2NNQ 1 REMARK REVDAT 5 27-DEC-23 2NNQ 1 REMARK SHEET REVDAT 4 18-OCT-17 2NNQ 1 REMARK REVDAT 3 20-JUN-12 2NNQ 1 REMARK VERSN REVDAT 2 24-FEB-09 2NNQ 1 VERSN REVDAT 1 12-JUN-07 2NNQ 0 JRNL AUTH R.SULSKY,D.R.MAGNIN,Y.HUANG,L.SIMPKINS,P.TAUNK,M.PATEL, JRNL AUTH 2 Y.ZHU,T.R.STOUCH,D.BASSOLINO-KLIMAS,R.PARKER,T.HARRITY, JRNL AUTH 3 R.STOFFEL,D.S.TAYLOR,T.B.LAVOIE,K.KISH,B.L.JACOBSON, JRNL AUTH 4 S.SHERIFF,L.P.ADAM,W.R.EWING,J.A.ROBL JRNL TITL POTENT AND SELECTIVE BIPHENYL AZOLE INHIBITORS OF ADIPOCYTE JRNL TITL 2 FATTY ACID BINDING PROTEIN (AFABP). JRNL REF BIOORG.MED.CHEM.LETT. V. 17 3511 2007 JRNL REFN ISSN 0960-894X JRNL PMID 17502136 JRNL DOI 10.1016/J.BMCL.2006.12.044 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 5.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2022639.620 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 84.1 REMARK 3 NUMBER OF REFLECTIONS : 10359 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1032 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.1930 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.1880 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1032 REMARK 3 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : 0.0070 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 10359 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.88 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 64.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 890 REMARK 3 BIN R VALUE (WORKING SET) : 0.2360 REMARK 3 BIN FREE R VALUE : 0.2740 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 95 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.028 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1014 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 152 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.58000 REMARK 3 B22 (A**2) : -1.57000 REMARK 3 B33 (A**2) : -1.01000 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) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.14 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 0.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.510 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.010 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.490 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.750 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.530 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : 0.56 REMARK 3 BSOL : 73.14 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : T4B.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : T4B.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2NNQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1000040085. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-99 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : BRUKER REMARK 200 INTENSITY-INTEGRATION SOFTWARE : X-GEN REMARK 200 DATA SCALING SOFTWARE : X-GEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12558 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.670 REMARK 200 RESOLUTION RANGE LOW (A) : 99.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 78.6 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 64.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.18300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MR REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: AP2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ~70% SATURATED AMMONIUM SULFATE, PH REMARK 280 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, PH 5.60 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 16.31000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.20500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.96500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.20500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.31000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.96500 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: MONOMERIC 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 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 GLU A 54 CB CG CD OE1 OE2 REMARK 470 LYS A 79 CD CE NZ 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 ASP A 110 -128.80 45.62 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 291 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 292 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE T4B A 293 DBREF 2NNQ A 1 131 UNP P15090 FABPA_HUMAN 1 131 SEQRES 1 A 131 CYS ASP ALA PHE VAL GLY THR TRP LYS LEU VAL SER SER SEQRES 2 A 131 GLU ASN PHE ASP ASP TYR MET LYS GLU VAL GLY VAL GLY SEQRES 3 A 131 PHE ALA THR ARG LYS VAL ALA GLY MET ALA LYS PRO ASN SEQRES 4 A 131 MET ILE ILE SER VAL ASN GLY ASP VAL ILE THR ILE LYS SEQRES 5 A 131 SER GLU SER THR PHE LYS ASN THR GLU ILE SER PHE ILE SEQRES 6 A 131 LEU GLY GLN GLU PHE ASP GLU VAL THR ALA ASP ASP ARG SEQRES 7 A 131 LYS VAL LYS SER THR ILE THR LEU ASP GLY GLY VAL LEU SEQRES 8 A 131 VAL HIS VAL GLN LYS TRP ASP GLY LYS SER THR THR ILE SEQRES 9 A 131 LYS ARG LYS ARG GLU ASP ASP LYS LEU VAL VAL GLU CYS SEQRES 10 A 131 VAL MET LYS GLY VAL THR SER THR ARG VAL TYR GLU ARG SEQRES 11 A 131 ALA HET SO4 A 291 5 HET SO4 A 292 5 HET T4B A 293 36 HETNAM SO4 SULFATE ION HETNAM T4B ((2'-(5-ETHYL-3,4-DIPHENYL-1H-PYRAZOL-1-YL)-3- HETNAM 2 T4B BIPHENYLYL)OXY)ACETIC ACID FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 T4B C31 H26 N2 O3 FORMUL 5 HOH *152(H2 O) HELIX 1 1 CYS A 1 VAL A 5 5 5 HELIX 2 2 ASN A 15 GLY A 24 1 10 HELIX 3 3 GLY A 26 ALA A 36 1 11 SHEET 1 A 9 THR A 60 PHE A 64 0 SHEET 2 A 9 VAL A 48 SER A 53 -1 N SER A 53 O THR A 60 SHEET 3 A 9 ASN A 39 ASN A 45 -1 N SER A 43 O THR A 50 SHEET 4 A 9 GLY A 6 GLU A 14 -1 N TRP A 8 O MET A 40 SHEET 5 A 9 VAL A 122 ARG A 130 -1 O VAL A 127 N VAL A 11 SHEET 6 A 9 LYS A 112 MET A 119 -1 N VAL A 115 O ARG A 126 SHEET 7 A 9 LYS A 100 GLU A 109 -1 N GLU A 109 O LYS A 112 SHEET 8 A 9 VAL A 90 TRP A 97 -1 N TRP A 97 O LYS A 100 SHEET 9 A 9 PHE A 70 VAL A 73 -1 N PHE A 70 O SER A 82 SITE 1 AC1 8 SER A 13 GLU A 14 ASN A 15 PHE A 16 SITE 2 AC1 8 ASP A 17 HOH A 302 HOH A 335 HOH A 368 SITE 1 AC2 10 LYS A 21 PHE A 27 ARG A 30 ARG A 108 SITE 2 AC2 10 ASP A 111 ARG A 130 HOH A 336 HOH A 345 SITE 3 AC2 10 HOH A 563 HOH A 682 SITE 1 AC3 14 ALA A 33 ALA A 36 PRO A 38 ILE A 51 SITE 2 AC3 14 SER A 53 ALA A 75 ASP A 76 ARG A 106 SITE 3 AC3 14 VAL A 115 CYS A 117 ARG A 126 TYR A 128 SITE 4 AC3 14 HOH A 634 HOH A 664 CRYST1 32.620 53.930 74.410 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 0.030656 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018543 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013439 0.00000