SMTL ID : 1fo4.1

CRYSTAL STRUCTURE OF XANTHINE DEHYDROGENASE ISOLATED FROM BOVINE MILK

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 8 residues within 4Å: Chain A: H.840, A.867, S.870, R.871, D.872, S.874, S.907, N.908 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:A.867, A:S.870, A:S.874, A:S.907, A:N.908 CA.10: 8 residues within 4Å: Chain B: H.840, A.867, S.870, R.871, D.872, S.874, S.907, N.908 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:A.867, B:S.870, B:S.874, B:S.907, B:N.908

4 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.2: 8 residues within 4Å: Chain A: Q.112, C.113, G.114, C.116, C.148, R.149, C.150, L.744 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.113, A:C.116, A:C.148, A:C.150 FES.3: 10 residues within 4Å: Chain A: G.42, C.43, G.44, G.46, G.47, C.48, G.49, C.51, N.71, C.73 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.43, A:C.48, A:C.51, A:C.73 FES.11: 8 residues within 4Å: Chain B: Q.112, C.113, G.114, C.116, C.148, R.149, C.150, L.744 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.113, B:C.116, B:C.148, B:C.150 FES.12: 10 residues within 4Å: Chain B: G.42, C.43, G.44, G.46, G.47, C.48, G.49, C.51, N.71, C.73 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.43, B:C.48, B:C.51, B:C.73

2 x MTE: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER(Non-covalent)

MTE.4: 20 residues within 4Å: Chain A: Q.112, C.150, G.796, G.797, F.798, G.799, R.912, M.1038, G.1039, Q.1040, A.1078, A.1079, S.1080, V.1081, S.1082, T.1083, Q.1194, G.1260, E.1261 Ligands: MOS.5 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:Q.112, A:G.797, A:F.798, A:M.1038, A:Q.1040, A:S.1082, A:S.1082, A:S.1082, A:T.1083, A:Q.1194, A:Q.1194 Water bridges: A:Q.112, A:R.912, A:T.1083, A:G.1260 MTE.13: 19 residues within 4Å: Chain B: Q.112, C.150, G.796, G.797, F.798, G.799, R.912, M.1038, G.1039, Q.1040, A.1078, A.1079, S.1080, V.1081, S.1082, Q.1194, G.1260, E.1261 Ligands: MOS.14 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:Q.112, B:G.797, B:F.798, B:M.1038, B:Q.1040, B:S.1082, B:S.1082, B:T.1083, B:T.1083, B:Q.1194, B:Q.1194 Water bridges: B:Q.112, B:R.912, B:G.1260

2 x MOS: DIOXOTHIOMOLYBDENUM(VI) ION(Non-covalent)

MOS.5: 11 residues within 4Å: Chain A: Q.767, F.798, G.799, E.802, F.911, R.912, T.1077, A.1078, A.1079, E.1261 Ligands: MTE.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.1079, A:E.1261 MOS.14: 12 residues within 4Å: Chain B: Q.767, F.798, G.799, E.802, A.910, F.911, R.912, T.1077, A.1078, A.1079, E.1261 Ligands: MTE.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.1079

2 x SAL: 2-HYDROXYBENZOIC ACID(Non-covalent)

SAL.6: 11 residues within 4Å: Chain A: E.802, L.873, S.876, R.880, F.914, S.1008, F.1009, T.1010, V.1011, L.1014, A.1079 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.873, A:L.1014 Hydrogen bonds: A:S.876, A:T.1010, A:T.1010, A:V.1011 Salt bridges: A:R.880 pi-Stacking: A:F.914, A:F.1009 SAL.15: 9 residues within 4Å: Chain B: E.802, S.876, R.880, F.914, S.1008, F.1009, T.1010, V.1011, A.1078 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.1078 Hydrogen bonds: B:S.876, B:T.1010, B:T.1010, B:T.1010, B:V.1011 Water bridges: B:R.880, B:A.1079 Salt bridges: B:R.880 pi-Stacking: B:F.914, B:F.1009

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.7: 32 residues within 4Å: Chain A: E.45, G.46, G.47, L.74, K.256, L.257, V.258, V.259, G.260, N.261, T.262, E.263, I.264, A.301, W.336, F.337, A.338, V.342, A.346, S.347, G.349, G.350, N.351, I.353, T.354, S.359, D.360, I.403, L.404, K.422, D.429, D.430 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:L.74, A:A.338 Hydrogen bonds: A:L.257, A:L.257, A:V.259, A:G.260, A:N.261, A:T.262, A:T.262, A:E.263, A:I.264, A:A.338, A:S.347, A:N.351, A:D.360, A:D.360, A:D.360, A:L.404, A:L.404 Water bridges: A:K.256, A:S.347, A:N.351 pi-Stacking: A:F.337 FAD.16: 31 residues within 4Å: Chain B: E.45, G.46, G.47, L.74, K.256, L.257, V.258, V.259, G.260, N.261, T.262, E.263, I.264, A.301, W.336, F.337, A.338, V.342, A.346, S.347, G.350, N.351, I.353, T.354, S.359, D.360, I.403, L.404, K.422, D.429, D.430 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:L.74, B:A.338 Hydrogen bonds: B:L.257, B:L.257, B:V.259, B:G.260, B:N.261, B:T.262, B:E.263, B:I.264, B:A.338, B:S.347, B:T.354, B:D.360, B:D.360, B:L.404, B:L.404 Water bridges: B:K.256, B:S.347, B:N.351, B:D.429, B:A.432 pi-Stacking: B:F.337

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 10 residues within 4Å: Chain A: R.839, H.840, I.877, T.909, A.910, F.911, G.913, F.914, G.915, Q.918 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.840, A:F.911, A:F.911, A:F.914, A:G.915, A:Q.918, A:Q.918 GOL.9: 4 residues within 4Å: Chain A: Q.561, G.574, S.1184, S.1185 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.1184, A:S.1185 Water bridges: A:V.563, A:D.1246 GOL.17: 11 residues within 4Å: Chain B: R.839, H.840, I.877, T.909, A.910, F.911, G.913, F.914, G.915, P.917, Q.918 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:H.840, B:H.840, B:F.911, B:F.911, B:F.914, B:G.915, B:Q.918, B:Q.918 GOL.18: 6 residues within 4Å: Chain B: Q.561, V.573, G.574, S.1184, S.1185, P.1188 5 PLIP interactions: 5 interactions with chain B Water bridges: B:V.563, B:S.1184, B:S.1185, B:S.1185, B:Y.1254

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Enroth, C. et al., Crystal structures of bovine milk xanthine dehydrogenase and xanthine oxidase: structure-based mechanism of conversion. Proc.Natl.Acad.Sci.USA (2000)

Release Date

2000-10-25

Peptides

XANTHINE DEHYDROGENASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

XANTHINE DEHYDROGENASE

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