SMTL ID : 7dqx.1

Crystal structure of xanthine dehydrogenase family protein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.44 Å

Oligo State

hetero-2-1-2-1-mer

Ligands

2 x MCN: PTERIN CYTOSINE DINUCLEOTIDE(Non-covalent)

MCN.1: 28 residues within 4Å: Chain A: G.267, S.268, F.269, G.270, R.383, V.511, G.512, Q.513, V.518, S.550, W.551, S.552, S.553, R.554, S.555, T.556, T.678, T.679, Q.682, G.745, L.746, G.747, E.748 Chain C: Q.100, C.101, C.139 Ligands: MO.2, FES.5 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:Q.513 Hydrogen bonds: A:S.268, A:F.269, A:R.383, A:Q.513, A:Q.513, A:S.550, A:W.551, A:S.553, A:S.553, A:R.554, A:S.555, A:S.555, A:T.678, A:Q.682, A:L.746, A:L.746, A:G.747, A:E.748, C:Q.100 MCN.9: 30 residues within 4Å: Chain E: Q.100, C.101, C.139 Chain F: G.267, S.268, F.269, G.270, R.383, V.511, G.512, Q.513, G.514, I.515, V.518, S.550, W.551, S.552, S.553, R.554, S.555, T.556, T.678, T.679, Q.682, G.745, L.746, G.747, E.748 Ligands: FES.8, MO.10 18 PLIP interactions: 17 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:S.268, F:F.269, F:R.383, F:R.383, F:Q.513, F:Q.513, F:S.550, F:S.553, F:S.553, F:R.554, F:S.555, F:S.555, F:T.678, F:Q.682, F:L.746, F:L.746, F:G.747, E:Q.100

2 x MO: MOLYBDENUM ATOM(Non-covalent)

MO.2: 3 residues within 4Å: Chain A: F.269, G.270 Ligands: MCN.1 Ligand excluded by PLIP MO.10: 3 residues within 4Å: Chain F: F.269, G.270 Ligands: MCN.9 Ligand excluded by PLIP

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

FAD.3: 29 residues within 4Å: Chain B: K.29, I.30, I.31, A.32, G.33, G.34, Q.35, S.36, L.37, H.78, I.101, A.102, I.106, G.110, T.111, G.113, G.114, S.115, A.117, H.118, A.123, E.124, L.166, I.167, G.191, Y.193 Chain C: H.44, G.45, V.46 24 PLIP interactions: 23 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:A.102, B:I.106, C:V.46 Hydrogen bonds: B:K.29, B:K.29, B:A.32, B:G.33, B:G.34, B:G.34, B:Q.35, B:S.36, B:S.36, B:L.37, B:A.102, B:T.111, B:T.111, B:T.111, B:S.115, B:H.118, B:E.124, B:E.124, B:I.167, B:I.167, B:Y.193 FAD.6: 25 residues within 4Å: Chain D: K.29, I.30, I.31, G.33, G.34, Q.35, S.36, L.37, H.78, I.101, A.102, I.106, G.110, T.111, G.113, G.114, S.115, A.117, A.122, A.123, E.124, L.166, I.167, Y.193 Chain F: M.713 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:I.101, D:I.101, D:A.123, D:E.124, D:Y.193 Hydrogen bonds: D:K.29, D:I.30, D:I.30, D:G.33, D:G.34, D:Q.35, D:Q.35, D:S.36, D:S.36, D:L.37, D:H.78, D:T.111, D:T.111, D:G.114, D:S.115, D:I.167, D:I.167

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

FES.4: 10 residues within 4Å: Chain C: V.40, C.42, E.43, G.45, V.46, C.47, G.48, C.50, R.60, C.62 5 PLIP interactions: 5 interactions with chain C, Metal complexes: C:C.42, C:C.47, C:C.50, C:C.50, C:C.62 FES.5: 8 residues within 4Å: Chain A: M.216 Chain C: Q.100, C.101, C.104, C.137, R.138, C.139 Ligands: MCN.1 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.101, C:C.104, C:C.137, C:C.139 FES.7: 10 residues within 4Å: Chain E: V.40, C.42, E.43, G.45, V.46, C.47, G.48, C.50, R.60, C.62 5 PLIP interactions: 5 interactions with chain E, Metal complexes: E:C.42, E:C.47, E:C.50, E:C.50, E:C.62 FES.8: 8 residues within 4Å: Chain E: Q.100, C.101, C.104, C.137, R.138, C.139 Chain F: M.216 Ligands: MCN.9 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.101, E:C.104, E:C.137, E:C.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lei, W., crystal structure of xanthine dehydrogenase family protein. To Be Published

Release Date

2022-01-26

Peptides

6-hydroxypseudooxynicotine dehydrogenase complex subunit gamma: AF
6-hydroxypseudooxynicotine dehydrogenase complex subunit alpha: B
6-hydroxypseudooxynicotine dehydrogenase complex subunit beta: CE
6-hydroxypseudooxynicotine dehydrogenase complex subunit alpha: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
D

B
B

C
C

E
F

D
E

6-hydroxypseudooxynicotine dehydrogenase complex subunit gamma

6-hydroxypseudooxynicotine dehydrogenase complex subunit alpha

6-hydroxypseudooxynicotine dehydrogenase complex subunit beta

6-hydroxypseudooxynicotine dehydrogenase complex subunit alpha