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

Crystal Structure of Xanthine Dehydrogenase from Rhodobacter capsulatus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-2-2-mer

Ligands

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

FES.1: 7 residues within 4Å: Chain A: Q.102, C.103, G.104, C.106, C.134, R.135, C.136 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.103, A:C.106, A:C.134, A:C.136 FES.2: 10 residues within 4Å: Chain A: E.37, G.38, C.39, N.40, G.42, D.43, C.44, G.45, C.47, C.63 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.39, A:C.44, A:C.47, A:C.63 FES.7: 9 residues within 4Å: Chain C: Q.102, C.103, G.104, C.106, C.134, R.135, C.136, T.137 Chain D: L.176 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.103, C:C.106, C:C.134, C:C.136 FES.8: 10 residues within 4Å: Chain C: G.38, C.39, N.40, G.42, D.43, C.44, G.45, C.47, N.61, C.63 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.39, C:C.44, C:C.47, C:C.63

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

FAD.3: 31 residues within 4Å: Chain A: E.41, G.42, D.43, L.201, I.202, A.203, G.204, G.205, T.206, D.207, V.208, W.211, L.225, R.269, F.270, A.271, V.275, A.279, T.280, G.283, N.284, A.286, N.287, G.292, D.293, R.330, F.335, V.336, K.352, Q.359, D.360 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:A.271, A:V.275 Hydrogen bonds: A:L.201, A:L.201, A:A.203, A:G.204, A:G.205, A:T.206, A:T.206, A:D.207, A:V.208, A:A.271, A:T.280, A:N.284, A:D.293, A:D.293, A:V.336, A:V.336, A:K.352 pi-Stacking: A:F.270 FAD.9: 32 residues within 4Å: Chain C: E.41, G.42, D.43, L.64, L.201, I.202, A.203, G.204, G.205, T.206, D.207, V.208, W.211, L.225, A.245, F.270, A.271, V.275, A.279, T.280, G.283, N.284, A.286, N.287, G.292, D.293, R.330, F.335, V.336, K.352, Q.359, D.360 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:L.64, C:A.271 Hydrogen bonds: C:L.201, C:A.203, C:G.204, C:G.205, C:T.206, C:D.207, C:D.207, C:V.208, C:A.271, C:T.280, C:N.284, C:D.293, C:D.293, C:D.293, C:V.336, C:V.336, C:K.352 pi-Stacking: C:F.270

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain B: E.172, H.173, Y.175, T.266, G.267 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.172, B:H.173, B:T.266, B:G.267 CA.10: 6 residues within 4Å: Chain D: E.172, H.173, Y.175, D.262, T.266, G.267 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.266

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.5: 20 residues within 4Å: Chain A: Q.102, C.136 Chain B: G.226, G.227, F.228, G.229, R.342, M.488, G.489, Q.490, T.527, A.528, A.529, S.530, S.531, G.532, A.533, Q.663, E.730 Ligands: MOS.6 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.227, B:F.228, B:M.488, B:Q.490, B:G.532, B:A.533, B:Q.663, B:Q.663, A:Q.102 MTE.11: 20 residues within 4Å: Chain C: Q.102, C.136 Chain D: G.226, G.227, F.228, G.229, R.342, M.488, G.489, Q.490, T.527, A.528, A.529, S.530, S.531, G.532, A.533, Q.663, E.730 Ligands: MOS.12 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.227, D:F.228, D:M.488, D:Q.490, D:G.532, D:A.533, D:Q.663, D:Q.663, C:Q.102

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

MOS.6: 10 residues within 4Å: Chain B: Q.197, G.229, E.232, F.341, R.342, G.343, A.528, A.529, E.730 Ligands: MTE.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.343, B:A.529, B:E.730 MOS.12: 11 residues within 4Å: Chain D: Q.197, F.228, G.229, F.341, R.342, F.344, T.527, A.528, A.529, E.730 Ligands: MTE.11 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.529, D:E.730

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Truglio, J.J. et al., Crystal structures of the active and alloxanthine-inhibited forms of xanthine dehydrogenase from Rhodobacter capsulatus. Structure (2002)

Release Date

2002-01-11

Peptides

xanthine dehydrogenase, chain A: AC
xanthine dehydrogenase, chain B: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

C
G

B
F

D
H

xanthine dehydrogenase, chain A

xanthine dehydrogenase, chain B

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