SMTL ID : 2w54.1 (3 other biounits)

Crystal Structure of Xanthine Dehydrogenase from Rhodobacter capsulatus in Complex with Bound Inhibitor Pterin-6-aldehyde

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.30 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: 9 residues within 4Å: Chain A: 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

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

FAD.3: 30 residues within 4Å: Chain A: E.41, G.42, D.43, L.201, 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 A Hydrophobic interactions: A:A.271, A:V.275 Hydrogen bonds: 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:N.287, A:D.293, A:D.293, A:V.336, A:V.336, A:K.352 pi-Stacking: A:F.270

1 x XAX: {[(5aR,8R,9aR)-2-amino-4-oxo-6,7-di(sulfanyl-kappaS)-3,5,5a,8,9a,10-hexahydro-4H-pyrano[3,2-g]pteridin-8-yl]methyl dihydrogenato(2-) phosphate}(hydroxy)oxo(thioxo)molybdenum(Non-covalent)

XAX.4: 25 residues within 4Å: Chain A: Q.102, C.136 Chain B: Q.197, G.226, G.227, F.228, G.229, E.232, F.341, 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: HHR.6 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.197, B:G.227, B:F.228, B:E.232, B:M.488, B:Q.490, B:A.529, B:S.530, B:G.532, B:A.533, B:Q.663, B:G.729, A:Q.102 pi-Cation interactions: B:R.342

1 x BA: BARIUM ION(Non-covalent)

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

1 x HHR: 6-HYDROXYMETHYLPTERIN(Non-covalent)

HHR.6: 12 residues within 4Å: Chain B: E.232, P.306, R.310, F.344, F.459, T.460, L.461, L.464, A.528, A.529, E.730 Ligands: XAX.4 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.310, B:R.310, B:T.460, B:A.529 Salt bridges: B:E.232, B:E.730 pi-Stacking: B:F.344, B:F.459, B:F.459 pi-Cation interactions: B:F.344

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
A

B
B

XANTHINE DEHYDROGENASE

XANTHINE DEHYDROGENASE

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