HEADER LIPID BINDING PROTEIN/INHIBITOR 19-NOV-13 4NNT TITLE CRYSTAL STRUCTURE OF FABP4 IN COMPLEX WITH NOVEL INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: FATTY ACID-BINDING PROTEIN, ADIPOCYTE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HEPATOCYTE GROWTH FACTOR RECEPTOR, ADIPOCYTE LIPID-BINDING COMPND 5 PROTEIN, ALBP, ADIPOCYTE-TYPE FATTY ACID-BINDING PROTEIN, A-FABP, COMPND 6 AFABP, FATTY ACID-BINDING PROTEIN 4; COMPND 7 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; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS FABP4 INHIBITOR, LIPID BINDING PROTEIN-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Q.F.LIU,T.T.CHEN,Y.C.XU REVDAT 3 20-MAR-24 4NNT 1 REMARK SEQADV REVDAT 2 20-SEP-17 4NNT 1 REMARK REVDAT 1 19-NOV-14 4NNT 0 JRNL AUTH Q.F.LIU,T.T.CHEN,Y.C.XU JRNL TITL THE COMPLEX STRUCTURE OF FABP4 WITH NOVEL INHIBITORS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 20574 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.000 REMARK 3 FREE R VALUE TEST SET COUNT : 618 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.8459 - 2.4285 0.99 5124 159 0.1913 0.2045 REMARK 3 2 2.4285 - 1.9277 1.00 4979 154 0.1879 0.2124 REMARK 3 3 1.9277 - 1.6840 1.00 4950 153 0.1908 0.2427 REMARK 3 4 1.6840 - 1.5300 1.00 4903 152 0.2077 0.2302 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.490 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.33 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1072 REMARK 3 ANGLE : 1.089 1443 REMARK 3 CHIRALITY : 0.072 166 REMARK 3 PLANARITY : 0.004 179 REMARK 3 DIHEDRAL : 11.756 405 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4NNT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-DEC-13. REMARK 100 THE DEPOSITION ID IS D_1000083434. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20653 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 REMARK 200 RESOLUTION RANGE LOW (A) : 29.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.46700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.1.4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6M NA-CITRATE, PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 16.24500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.72000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.93500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.72000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.24500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.93500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 MET A -20 REMARK 465 GLY A -19 REMARK 465 SER A -18 REMARK 465 SER A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 SER A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 REMARK 465 LEU A -7 REMARK 465 VAL A -6 REMARK 465 PRO A -5 REMARK 465 ARG A -4 REMARK 465 GLY A -3 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 14 CD OE1 OE2 REMARK 470 LYS A 37 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 -127.21 49.00 REMARK 500 LYS A 120 -114.93 53.32 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 76D A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NNS RELATED DB: PDB DBREF 4NNT A 0 131 UNP P15090 FABP4_HUMAN 1 132 SEQADV 4NNT MET A -20 UNP P15090 EXPRESSION TAG SEQADV 4NNT GLY A -19 UNP P15090 EXPRESSION TAG SEQADV 4NNT SER A -18 UNP P15090 EXPRESSION TAG SEQADV 4NNT SER A -17 UNP P15090 EXPRESSION TAG SEQADV 4NNT HIS A -16 UNP P15090 EXPRESSION TAG SEQADV 4NNT HIS A -15 UNP P15090 EXPRESSION TAG SEQADV 4NNT HIS A -14 UNP P15090 EXPRESSION TAG SEQADV 4NNT HIS A -13 UNP P15090 EXPRESSION TAG SEQADV 4NNT HIS A -12 UNP P15090 EXPRESSION TAG SEQADV 4NNT HIS A -11 UNP P15090 EXPRESSION TAG SEQADV 4NNT SER A -10 UNP P15090 EXPRESSION TAG SEQADV 4NNT SER A -9 UNP P15090 EXPRESSION TAG SEQADV 4NNT GLY A -8 UNP P15090 EXPRESSION TAG SEQADV 4NNT LEU A -7 UNP P15090 EXPRESSION TAG SEQADV 4NNT VAL A -6 UNP P15090 EXPRESSION TAG SEQADV 4NNT PRO A -5 UNP P15090 EXPRESSION TAG SEQADV 4NNT ARG A -4 UNP P15090 EXPRESSION TAG SEQADV 4NNT GLY A -3 UNP P15090 EXPRESSION TAG SEQADV 4NNT SER A -2 UNP P15090 EXPRESSION TAG SEQADV 4NNT HIS A -1 UNP P15090 EXPRESSION TAG SEQRES 1 A 152 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 152 LEU VAL PRO ARG GLY SER HIS MET CYS ASP ALA PHE VAL SEQRES 3 A 152 GLY THR TRP LYS LEU VAL SER SER GLU ASN PHE ASP ASP SEQRES 4 A 152 TYR MET LYS GLU VAL GLY VAL GLY PHE ALA THR ARG LYS SEQRES 5 A 152 VAL ALA GLY MET ALA LYS PRO ASN MET ILE ILE SER VAL SEQRES 6 A 152 ASN GLY ASP VAL ILE THR ILE LYS SER GLU SER THR PHE SEQRES 7 A 152 LYS ASN THR GLU ILE SER PHE ILE LEU GLY GLN GLU PHE SEQRES 8 A 152 ASP GLU VAL THR ALA ASP ASP ARG LYS VAL LYS SER THR SEQRES 9 A 152 ILE THR LEU ASP GLY GLY VAL LEU VAL HIS VAL GLN LYS SEQRES 10 A 152 TRP ASP GLY LYS SER THR THR ILE LYS ARG LYS ARG GLU SEQRES 11 A 152 ASP ASP LYS LEU VAL VAL GLU CYS VAL MET LYS GLY VAL SEQRES 12 A 152 THR SER THR ARG VAL TYR GLU ARG ALA HET 76D A 201 18 HETNAM 76D 2,4,6-TRI(PROPAN-2-YL)BENZOIC ACID HETSYN 76D 2,4,6-TRIISOPROPYLBENZOIC ACID FORMUL 2 76D C16 H24 O2 FORMUL 3 HOH *124(H2 O) HELIX 1 1 HIS A -1 VAL A 5 5 7 HELIX 2 2 ASN A 15 GLY A 24 1 10 HELIX 3 3 GLY A 26 ALA A 36 1 11 SHEET 1 A10 ASN A 59 ILE A 65 0 SHEET 2 A10 VAL A 48 GLU A 54 -1 N ILE A 49 O PHE A 64 SHEET 3 A10 ASN A 39 ASN A 45 -1 N ILE A 41 O LYS A 52 SHEET 4 A10 GLY A 6 GLU A 14 -1 N TRP A 8 O MET A 40 SHEET 5 A10 VAL A 122 ARG A 130 -1 O VAL A 127 N VAL A 11 SHEET 6 A10 LYS A 112 MET A 119 -1 N VAL A 115 O ARG A 126 SHEET 7 A10 LYS A 100 GLU A 109 -1 N LYS A 107 O VAL A 114 SHEET 8 A10 VAL A 90 TRP A 97 -1 N TRP A 97 O LYS A 100 SHEET 9 A10 LYS A 79 ASP A 87 -1 N THR A 85 O VAL A 92 SHEET 10 A10 PHE A 70 VAL A 73 -1 N PHE A 70 O SER A 82 SITE 1 AC1 10 MET A 20 ALA A 33 SER A 53 ALA A 75 SITE 2 AC1 10 CYS A 117 ARG A 126 TYR A 128 HOH A 316 SITE 3 AC1 10 HOH A 326 HOH A 332 CRYST1 32.490 53.870 75.440 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 0.030779 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018563 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013256 0.00000