SMTL ID : 2e1q.1 (1 other biounit)

Crystal Structure of Human Xanthine Oxidoreductase mutant, Glu803Val

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.1: 9 residues within 4Å: Chain A: R.840, H.841, I.878, T.910, A.911, F.912, F.915, G.916, Q.919 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.840, A:F.912, A:G.916, A:Q.919 BCT.10: 8 residues within 4Å: Chain B: R.840, H.841, I.878, T.910, F.912, F.915, G.916, Q.919 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.841, B:H.841, B:T.910, B:Q.919, B:Q.919

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: E.741, H.742, Y.744, T.837, G.838 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.741, A:H.742, A:Y.744, A:T.837, A:G.838 CA.3: 6 residues within 4Å: Chain A: V.765, T.767, T.773, S.806, T.807, S.810 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.773, A:S.806, A:S.810 CA.11: 5 residues within 4Å: Chain B: E.741, H.742, Y.744, T.837, G.838 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.742, B:Y.744, B:T.837, B:G.838 CA.12: 5 residues within 4Å: Chain B: V.765, T.773, S.806, T.807, S.810 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.773, B:S.806, B:S.810

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

FES.4: 9 residues within 4Å: Chain A: Q.112, C.113, G.114, C.116, C.148, R.149, C.150, T.151, L.745 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.113, A:C.116, A:C.148, A:C.150 FES.5: 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.13: 8 residues within 4Å: Chain B: Q.112, C.113, G.114, C.116, C.148, R.149, C.150, L.745 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.113, B:C.116, B:C.148, B:C.150 FES.14: 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 FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.6: 31 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.350, N.351, I.353, T.354, S.359, D.360, I.403, L.404, K.422, D.429, D.430 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:L.74, A:A.338, A:V.342 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:N.351, A:T.354, A:T.354, A:D.360, A:D.360, A:L.404, A:L.404 Water bridges: A:E.267, A:E.267, A:K.422, A:K.422 pi-Stacking: A:F.337 FAD.15: 32 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, I.358, S.359, D.360, I.403, L.404, K.422, D.429, D.430 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:L.74, B:A.338, B:V.342 Hydrogen bonds: B:L.257, B:V.259, B:G.260, B:N.261, B:T.262, B:T.262, B:E.263, B:I.264, B:A.338, B:S.347, B:N.351, B:T.354, B:D.360, B:D.360, B:D.360, B:L.404, B:L.404 Water bridges: B:S.347, B:N.351, B:S.359, B:K.422, B:K.422 pi-Stacking: B:F.337

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.7: 20 residues within 4Å: Chain A: Q.112, C.150, G.797, G.798, F.799, G.800, R.913, M.1039, G.1040, Q.1041, A.1079, A.1080, S.1081, V.1082, S.1083, A.1084, Q.1195, G.1261, E.1262 Ligands: MOM.8 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Q.112, A:G.798, A:F.799, A:M.1039, A:Q.1041, A:S.1081, A:S.1083, A:S.1083, A:A.1084, A:Q.1195, A:Q.1195 Water bridges: A:Q.112, A:R.913 MTE.16: 18 residues within 4Å: Chain B: Q.112, C.150, G.797, G.798, F.799, G.800, R.913, M.1039, G.1040, Q.1041, A.1079, A.1080, S.1081, V.1082, S.1083, Q.1195, E.1262 Ligands: MOM.17 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:Q.112, B:C.113, B:G.798, B:F.799, B:M.1039, B:Q.1041, B:S.1081, B:S.1083, B:S.1083, B:Q.1195, B:Q.1195 Water bridges: B:R.913, B:R.913, B:A.1084

2 x MOM: HYDROXY(DIOXO)MOLYBDENUM(Non-covalent)

MOM.8: 11 residues within 4Å: Chain A: Q.768, F.799, G.800, V.803, F.912, R.913, T.1078, A.1079, A.1080, E.1262 Ligands: MTE.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.768, A:A.1080, A:E.1262 MOM.17: 11 residues within 4Å: Chain B: Q.768, F.799, G.800, V.803, F.912, R.913, T.1078, A.1079, A.1080, E.1262 Ligands: MTE.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.768, B:A.1080, B:E.1262

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

SAL.9: 7 residues within 4Å: Chain A: R.881, F.915, F.1010, T.1011, V.1012, L.1015, A.1080 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.1015 Hydrogen bonds: A:T.1011, A:T.1011, A:V.1012 Salt bridges: A:R.881 pi-Stacking: A:F.915, A:F.1010 SAL.18: 7 residues within 4Å: Chain B: R.881, F.915, S.1009, F.1010, T.1011, V.1012, A.1080 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.1011, B:V.1012 Salt bridges: B:R.881 pi-Stacking: B:F.915, B:F.1010

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamaguchi, Y. et al., Human xanthine oxidase changes its substrate specificity to aldehyde oxidase type upon mutation of amino acid residues in the active site: roles of active site residues in binding and activation of purine substrate. J.Biochem.(Tokyo) (2007)

Release Date

2007-09-18

Peptides

Xanthine dehydrogenase/oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Xanthine dehydrogenase/oxidase

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