SMTL ID : 2w3s.3 (3 other biounits)

Crystal Structure of Xanthine Dehydrogenase (desulfo form) from Rhodobacter capsulatus in Complex with Xanthine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-mer

Ligands

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-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: 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 A, Metal complexes: A:C.39, A:C.44, A:C.47, A:C.63

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

FAD.3: 31 residues within 4Å: Chain A: 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, 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 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:L.64, 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: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

1 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: 22 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, L.492, T.527, A.528, A.529, S.530, S.531, G.532, A.533, Q.663, G.729, E.730 Ligands: MOM.7 9 PLIP interactions: 1 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:Q.102, B:G.227, B:F.228, B:M.488, B:Q.490, B:G.532, B:A.533, B:Q.663, B:Q.663

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain B: E.172, H.173, Y.175, T.266, G.267 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.172, B:T.266, B:G.267

1 x XAN: XANTHINE(Non-covalent)

XAN.6: 9 residues within 4Å: Chain B: E.232, F.344, F.459, T.460, L.461, L.464, A.528, A.529 Ligands: MOM.7 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.232, B:E.232, B:T.460, B:L.461 pi-Stacking: B:F.344, B:F.459, B:F.459

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

MOM.7: 11 residues within 4Å: Chain B: Q.197, F.228, G.229, E.232, F.341, R.342, A.528, A.529, E.730 Ligands: MTE.4, XAN.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.197, B:G.343, B:A.529, B:E.730

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dietzel, U. et al., Mechanism of Substrate and Inhibitor Binding of Rhodobacter Capsulatus Xanthine Dehydrogenase. J.Biol.Chem. (2009)

Release Date

2008-12-23

Peptides

XANTHINE DEHYDROGENASE: A
XANTHINE DEHYDROGENASE: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

XANTHINE DEHYDROGENASE

XANTHINE DEHYDROGENASE

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