10 20 30 40 50 60 70 80 2MM3 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER LIPID BINDING PROTEIN 07-MAR-14 2MM3
TITLE SOLUTION NMR STRUCTURE OF THE TERNARY COMPLEX OF HUMAN ILEAL BILE TITLE 2 ACID-BINDING PROTEIN WITH GLYCOCHOLATE AND GLYCOCHENODEOXYCHOLATE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: GASTROTROPIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ILEAL LIPID-BINDING PROTEIN; 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: FABP6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PMON5840
KEYWDS LIPID-BINDING PROTEIN, ORTHOGONAL BETA SHEETS, POSITIVE BINDING KEYWDS 2 COOPERATIVITY, SITE-SELECTIVITY, ENTEROHEPATIC CIRCULATION, LIPID KEYWDS 3 BINDING PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR G.HORVATH,O.EGYED,A.BENCSURA,A.SIMON,G.P.TOCHTROP,G.T.DEKOSTER, AUTHOR 2 D.F.COVEY,D.P.CISTOLA,O.TOKE
REVDAT 2 30-DEC-15 2MM3 1 JRNL REVDAT 1 07-MAY-14 2MM3 0
JRNL AUTH G.HORVATH,A.BENCSURA,A.SIMON,G.P.TOCHTROP,G.T.DEKOSTER, JRNL AUTH 2 D.F.COVEY,D.P.CISTOLA,O.TOKE JRNL TITL STRUCTURAL DETERMINANTS OF LIGAND BINDING IN THE TERNARY JRNL TITL 2 COMPLEX OF HUMAN ILEAL BILE ACID-BINDING PROTEIN WITH JRNL TITL 3 GLYCOCHOLATE AND GLYCOCHENODEOXYCHOLATE OBTAINED FROM JRNL TITL 4 SOLUTION NMR JRNL REF FEBS J. 2015 JRNL REFN ISSN 1742-464X JRNL PMID 26613247 JRNL DOI 10.1111/FEBS.13610
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH O.TOKE,J.D.MONSEY,G.T.DEKOSTER,G.P.TOCHTROP,C.TANG, REMARK 1 AUTH 2 D.P.CISTOLA REMARK 1 TITL DETERMINANTS OF COOPERATIVITY AND SITE SELECTIVITY IN HUMAN REMARK 1 TITL 2 ILEAL BILE ACID BINDING PROTEIN. REMARK 1 REF BIOCHEMISTRY V. 45 727 2006 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 16411748 REMARK 1 DOI 10.1021/BI051781P REMARK 1 REFERENCE 2 REMARK 1 AUTH G.P.TOCHTROP,G.T.DEKOSTER,D.F.COVEY,D.P.CISTOLA REMARK 1 TITL A SINGLE HYDROXYL GROUP GOVERNS LIGAND SITE SELECTIVITY IN REMARK 1 TITL 2 HUMAN ILEAL BILE ACID BINDING PROTEIN. REMARK 1 REF J.AM.CHEM.SOC. V. 126 11024 2004 REMARK 1 REFN ISSN 0002-7863 REMARK 1 PMID 15339188 REMARK 1 DOI 10.1021/JA047589C REMARK 1 REFERENCE 3 REMARK 1 AUTH O.TOKE,J.D.MONSEY,D.P.CISTOLA REMARK 1 TITL KINETIC MECHANISM OF LIGAND BINDING IN HUMAN ILEAL BILE ACID REMARK 1 TITL 2 BINDING PROTEIN AS DETERMINED BY STOPPED-FLOW FLUORESCENCE REMARK 1 TITL 3 ANALYSIS. REMARK 1 REF BIOCHEMISTRY V. 46 5427 2007 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 17432832 REMARK 1 DOI 10.1021/BI700030R REMARK 1 REFERENCE 4 REMARK 1 AUTH G.HORVATH,P.KIRALY,G.TARKANYI,O.TOKE REMARK 1 TITL INTERNAL MOTIONS AND EXCHANGE PROCESSES IN HUMAN ILEAL BILE REMARK 1 TITL 2 ACID BINDING PROTEIN AS STUDIED BY BACKBONE (15)N NUCLEAR REMARK 1 TITL 3 MAGNETIC RESONANCE SPECTROSCOPY. REMARK 1 REF BIOCHEMISTRY V. 51 1848 2012 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 22329738 REMARK 1 DOI 10.1021/BI201588Q REMARK 1 REFERENCE 5 REMARK 1 AUTH G.HORVATH,P.KIRALY,G.TARKANYI,O.TOKE REMARK 1 TITL INTERNAL MOTIONS AND EXCHANGE PROCESSES IN HUMAN ILEAL BILE REMARK 1 TITL 2 ACID BINDING PROTEIN AS STUDIED BY BACKBONE (15)N NUCLEAR REMARK 1 TITL 3 MAGNETIC RESONANCE SPECTROSCOPY REMARK 1 REF BIOCHEMISTRY V. 51 1848 2012 REMARK 1 REFN ISSN 0006-2960
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 2.1 REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2MM3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-MAR-14. REMARK 100 THE RCSB ID CODE IS RCSB103776.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.3 REMARK 210 IONIC STRENGTH : 70 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.0 MM [U-13C; U-15N] HUMAN REMARK 210 ILEAL BILE ACID-BINDING PROTEIN- REMARK 210 1, 1.5 MM GLYCOCHOLIC ACID-2, 1.5 REMARK 210 MM GLYCOCHENODEOXYCHOLIC ACID-3, REMARK 210 20 MM POTASSIUM PHOSPHATE-4, 50 REMARK 210 MM POTASSIUM CHLORIDE-5, 0.05 % REMARK 210 SODIUM AZIDE-6, 90% H2O/10% D2O; REMARK 210 1.0 MM HUMAN ILEAL BILE ACID- REMARK 210 BINDING PROTEIN-7, 1.5 MM [U-15N] REMARK 210 GLYCOCHOLIC ACID-8, 1.5 MM [U- REMARK 210 15N] GLYCOCHENODEOXYCHOLIC ACID- REMARK 210 9, 20 MM POTASSIUM PHOSPHATE-10, REMARK 210 50 MM POTASSIUM CHLORIDE-11, 0.05 REMARK 210 % SODIUM AZIDE-12, 90% H2O/10% REMARK 210 D2O; 1.0 MM HUMAN ILEAL BILE ACID REMARK 210 -BINDING PROTEIN-13, 1.5 MM 1',2' REMARK 210 -13C GLYCOCHOLIC ACID-14, 1.5 MM REMARK 210 1',2'-13C GLYCOCHENODEOXYCHOLIC REMARK 210 ACID-15, 20 MM POTASSIUM REMARK 210 PHOSPHATE-16, 50 MM POTASSIUM REMARK 210 CHLORIDE-17, 0.05 % SODIUM AZIDE- REMARK 210 18, 90% H2O/10% D2O; 1.0 MM HUMAN REMARK 210 ILEAL BILE ACID-BINDING PROTEIN- REMARK 210 19, 1.5 MM 3,4-13C GLYCOCHOLIC REMARK 210 ACID-20, 1.5 MM 3,4-13C REMARK 210 GLYCOCHENODEOXYCHOLIC ACID-21, 20 REMARK 210 MM POTASSIUM PHOSPHATE-22, 50 MM REMARK 210 POTASSIUM CHLORIDE-23, 0.05 % REMARK 210 SODIUM AZIDE-24, 90% H2O/10% D2O; REMARK 210 1.0 MM HUMAN ILEAL BILE ACID- REMARK 210 BINDING PROTEIN-25, 1.5 MM 23,24- REMARK 210 13C GLYCOCHOLIC ACID-26, 1.5 MM REMARK 210 23,24-13C GLYCOCHENODEOXYCHOLIC REMARK 210 ACID-27, 20 MM POTASSIUM REMARK 210 PHOSPHATE-28, 50 MM POTASSIUM REMARK 210 CHLORIDE-29, 0.05 % SODIUM AZIDE- REMARK 210 30, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HNCO; CBCACOCAHA; REMARK 210 HN(CO)CA; 3D CC-TOCSY-NNH; 3D HCC REMARK 210 -TOCSY; 3D HCCH-TOCSY; 2D CG(CB) REMARK 210 HB; 2D CG(CD)HD; 2D CG(CDCE)HE; REMARK 210 2D 1H-13C HSQC ALIPHATIC; 2D 1H- REMARK 210 13C HSQC AROMATIC; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY ALIPHATIC; REMARK 210 3D 1H-13C NOESY AROMATIC; 3D NH- REMARK 210 NH NOESY; 3D MET-MET NOESY; 2D REMARK 210 15N-EDITED NOESY; 2D 13C-EDITED REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : VARIAN NMR SYSTEM REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMRJ, FELIX, ARIA 2.1 REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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 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: 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 GLU A 9 67.10 -157.48 REMARK 500 1 SER A 10 126.77 -177.83 REMARK 500 1 SER A 25 -16.51 -156.55 REMARK 500 1 LYS A 35 106.17 51.37 REMARK 500 1 ILE A 36 150.96 -34.21 REMARK 500 1 SER A 54 -51.94 -23.72 REMARK 500 1 LEU A 126 41.34 -150.86 REMARK 500 2 GLU A 11 46.61 -173.52 REMARK 500 2 SER A 25 -22.03 -155.88 REMARK 500 2 LYS A 35 160.99 65.20 REMARK 500 2 SER A 54 -123.75 37.58 REMARK 500 2 LEU A 126 22.68 -149.05 REMARK 500 3 SER A 10 90.89 -168.37 REMARK 500 3 ASN A 13 19.14 55.67 REMARK 500 3 SER A 25 -24.86 -146.84 REMARK 500 3 ASN A 33 -84.91 -105.15 REMARK 500 3 LYS A 35 127.28 64.65 REMARK 500 3 SER A 54 28.15 49.61 REMARK 500 3 GLU A 120 72.86 -157.90 REMARK 500 3 LEU A 126 17.21 -157.97 REMARK 500 4 THR A 3 144.64 -29.52 REMARK 500 4 SER A 25 -32.72 -146.26 REMARK 500 4 PHE A 34 -8.50 -140.90 REMARK 500 4 LYS A 35 132.92 68.07 REMARK 500 4 TYR A 53 65.54 -63.88 REMARK 500 4 SER A 54 8.33 59.22 REMARK 500 4 HIS A 57 123.00 -170.35 REMARK 500 4 MET A 74 7.38 -63.57 REMARK 500 4 THR A 100 118.91 -167.54 REMARK 500 4 LEU A 126 25.46 -156.99 REMARK 500 5 THR A 3 139.18 -24.19 REMARK 500 5 SER A 10 105.12 -168.31 REMARK 500 5 LYS A 12 76.07 -158.17 REMARK 500 5 SER A 25 -34.47 -132.37 REMARK 500 5 ASP A 26 -76.49 -35.37 REMARK 500 5 PHE A 34 -90.58 -110.81 REMARK 500 5 LYS A 35 177.28 170.77 REMARK 500 5 HIS A 57 143.59 171.54 REMARK 500 5 MET A 85 62.22 -117.09 REMARK 500 5 GLU A 86 96.19 -68.94 REMARK 500 5 LEU A 126 9.78 -150.37 REMARK 500 6 GLU A 9 69.40 -160.71 REMARK 500 6 SER A 10 107.82 -167.41 REMARK 500 6 ASN A 13 26.31 93.82 REMARK 500 6 SER A 25 -33.18 -152.87 REMARK 500 6 LYS A 35 125.81 56.98 REMARK 500 6 ASN A 70 21.67 -152.55 REMARK 500 6 THR A 100 115.70 -162.20 REMARK 500 6 LEU A 126 -10.97 -154.35 REMARK 500 7 THR A 3 135.33 -35.92 REMARK 500 REMARK 500 THIS ENTRY HAS 77 RAMACHANDRAN OUTLIERS. 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 GCH A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CHO A 202
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19843 RELATED DB: BMRB
DBREF 2MM3 A 1 127 UNP P51161 FABP6_HUMAN 2 128
SEQRES 1 A 127 ALA PHE THR GLY LYS PHE GLU MET GLU SER GLU LYS ASN SEQRES 2 A 127 TYR ASP GLU PHE MET LYS LEU LEU GLY ILE SER SER ASP SEQRES 3 A 127 VAL ILE GLU LYS ALA ARG ASN PHE LYS ILE VAL THR GLU SEQRES 4 A 127 VAL GLN GLN ASP GLY GLN ASP PHE THR TRP SER GLN HIS SEQRES 5 A 127 TYR SER GLY GLY HIS THR MET THR ASN LYS PHE THR VAL SEQRES 6 A 127 GLY LYS GLU SER ASN ILE GLN THR MET GLY GLY LYS THR SEQRES 7 A 127 PHE LYS ALA THR VAL GLN MET GLU GLY GLY LYS LEU VAL SEQRES 8 A 127 VAL ASN PHE PRO ASN TYR HIS GLN THR SER GLU ILE VAL SEQRES 9 A 127 GLY ASP LYS LEU VAL GLU VAL SER THR ILE GLY GLY VAL SEQRES 10 A 127 THR TYR GLU ARG VAL SER LYS ARG LEU ALA
HET GCH A 201 75 HET CHO A 202 74
HETNAM GCH GLYCOCHOLIC ACID HETNAM CHO GLYCOCHENODEOXYCHOLIC ACID
HETSYN GCH N-CHOLYLGLYCINE
FORMUL 2 GCH C26 H43 N O6 FORMUL 3 CHO C26 H43 N O5
HELIX 1 1 ASN A 13 GLY A 22 1 10 HELIX 2 2 SER A 25 LYS A 35 1 11
SHEET 1 A 7 HIS A 57 THR A 64 0 SHEET 2 A 7 ASP A 46 TYR A 53 -1 N GLN A 51 O MET A 59 SHEET 3 A 7 VAL A 37 ASP A 43 -1 N GLN A 41 O THR A 48 SHEET 4 A 7 GLY A 4 LYS A 12 -1 N GLY A 4 O VAL A 40 SHEET 5 A 7 VAL A 117 ARG A 125 -1 O LYS A 124 N GLU A 7 SHEET 6 A 7 LYS A 107 ILE A 114 -1 N SER A 112 O TYR A 119 SHEET 7 A 7 TYR A 97 VAL A 104 -1 N VAL A 104 O LYS A 107 SHEET 1 B 2 ILE A 71 GLN A 72 0 SHEET 2 B 2 THR A 78 PHE A 79 -1 O PHE A 79 N ILE A 71 SHEET 1 C 2 GLN A 84 MET A 85 0 SHEET 2 C 2 LEU A 90 VAL A 91 -1 O VAL A 91 N GLN A 84
SITE 1 AC1 22 PHE A 2 PHE A 6 MET A 8 MET A 18 SITE 2 AC1 22 ALA A 31 ILE A 36 THR A 38 VAL A 40 SITE 3 AC1 22 PHE A 47 TRP A 49 GLN A 51 MET A 74 SITE 4 AC1 22 LEU A 90 SER A 101 GLU A 102 LEU A 108 SITE 5 AC1 22 VAL A 109 GLU A 110 TYR A 119 ARG A 121 SITE 6 AC1 22 SER A 123 CHO A 202 SITE 1 AC2 17 LEU A 21 ILE A 23 TRP A 49 ASN A 61 SITE 2 AC2 17 PHE A 63 GLN A 72 THR A 73 MET A 74 SITE 3 AC2 17 GLY A 75 LYS A 77 PHE A 79 VAL A 83 SITE 4 AC2 17 LEU A 90 VAL A 92 TYR A 97 GLN A 99 SITE 5 AC2 17 GCH A 201
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