SMTL ID : 2w55.3 (3 other biounits)

Crystal Structure of Xanthine Dehydrogenase (E232Q variant) from Rhodobacter capsulatus in Complex with Hypoxanthine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

hetero-1-1-mer

Ligands

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

FES.1: 8 residues within 4Å: Chain A: Q.102, C.103, G.104, C.106, C.134, R.135, C.136 Chain B: L.176 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, A.46, C.47, C.63 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.44, A:C.47, A:C.63

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

FAD.3: 32 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, 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 25 PLIP interactions: 25 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:D.207, A:V.208, A:A.271, A:T.280, A:N.284, A:N.287, A:D.293, A:D.293, A:G.294, A:R.330, A:V.336, A:V.336, A:K.352, 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, Q.232, F.341, R.342, G.343, M.488, G.489, Q.490, T.527, A.528, A.529, S.530, S.531, G.532, A.533, Q.663, G.729, E.730 Ligands: HPA.6 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.197, B:G.227, B:F.228, B:M.488, B:Q.490, B:A.529, B:S.530, B:S.530, B:G.532, B:A.533, B:Q.663, A:Q.102

1 x BA: BARIUM ION(Non-covalent)

BA.5: 6 residues within 4Å: Chain B: E.172, H.173, Y.175, D.262, T.266, G.267 No protein-ligand interaction detected (PLIP)

1 x HPA: HYPOXANTHINE(Non-covalent)

HPA.6: 11 residues within 4Å: Chain B: Q.232, P.306, R.310, F.344, S.458, F.459, T.460, L.461, A.528, A.529 Ligands: XAX.4 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Q.232, B:R.310, B:R.310, B:T.460, B:T.460 pi-Stacking: B:F.344, B:F.344, B:F.459, B:F.459

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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