SMTL ID : 3h8l.1

The first X-ray structure of a sulfide:quinone oxidoreductase: insights into sulfide oxidation mechanism

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.57 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.1: 27 residues within 4Å: Chain A: G.8, G.9, R.10, F.11, G.12, N.34, K.35, A.44, G.76, T.77, V.78, G.108, I.109, G.110, V.128, C.129, C.178, P.181, N.271, G.306, D.307, K.315, L.316, G.317, Y.318, A.320 Ligands: PO4.5 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:A.44, A:V.128, A:P.181 Hydrogen bonds: A:G.9, A:R.10, A:G.12, A:N.34, A:K.35, A:V.78, A:V.78, A:N.271, A:D.307, A:K.315, A:G.317, A:Y.318 Water bridges: A:R.10, A:A.13, A:N.34, A:S.36, A:G.110, A:A.111, A:Y.268, A:A.308 Salt bridges: A:R.10 FAD.8: 27 residues within 4Å: Chain B: G.8, G.9, R.10, F.11, G.12, N.34, K.35, A.44, G.76, T.77, V.78, G.108, I.109, G.110, V.128, C.129, C.178, P.181, N.271, G.306, D.307, K.315, L.316, G.317, Y.318, A.320 Ligands: PO4.7 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:A.44, B:V.128, B:P.181 Hydrogen bonds: B:G.9, B:R.10, B:G.12, B:N.34, B:K.35, B:V.78, B:V.78, B:N.271, B:D.307, B:K.315, B:G.317, B:Y.318 Water bridges: B:R.10, B:A.13, B:A.111, B:A.111, B:A.308, B:L.316 Salt bridges: B:R.10 pi-Cation interactions: B:K.35

2 x S3H: TRISULFANE(Non-covalent)

S3H.2: 7 residues within 4Å: Chain A: C.178, E.179, G.180, P.181, K.315, L.316, C.350 No protein-ligand interaction detected (PLIP) S3H.9: 7 residues within 4Å: Chain B: C.178, E.179, G.180, P.181, K.315, L.316, C.350 No protein-ligand interaction detected (PLIP)

9 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 4 residues within 4Å: Chain A: S.36, R.37, F.38, E.75 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.37, A:F.38 Water bridges: A:E.75 PO4.4: 6 residues within 4Å: Chain A: H.190, K.194, L.199, Q.230, L.231 Chain B: K.343 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Water bridges: B:K.343, A:H.190, A:L.231 Salt bridges: B:K.343, A:H.190, A:K.194 PO4.5: 6 residues within 4Å: Chain A: K.35, A.111, H.112, N.271, P.272 Ligands: FAD.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.111 Water bridges: A:N.271 Salt bridges: A:K.35, A:H.112 PO4.6: 4 residues within 4Å: Chain A: P.155, F.156, Y.157, K.240 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.157 Salt bridges: A:K.240 PO4.7: 5 residues within 4Å: Chain B: A.111, H.112, N.271, P.272 Ligands: FAD.8 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:A.111 Water bridges: B:L.113, B:L.113, B:N.271, B:N.271 Salt bridges: B:K.35, B:H.112 PO4.10: 4 residues within 4Å: Chain B: S.36, R.37, F.38, E.75 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.37, B:F.38 PO4.11: 6 residues within 4Å: Chain A: K.343 Chain B: H.190, K.194, L.199, Q.230, L.231 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:K.343 Salt bridges: A:K.343, B:H.190, B:K.194 PO4.12: 3 residues within 4Å: Chain B: S.85, Y.89, E.99 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.85, B:Y.89 PO4.13: 3 residues within 4Å: Chain B: K.92, D.94, S.96 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.94, B:D.94, B:S.96 Water bridges: B:Q.74, B:K.92 Salt bridges: B:K.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brito, J.A. et al., Structural and functional insights into sulfide:quinone oxidoreductase. Biochemistry (2009)

Release Date

2009-06-02

Peptides

NADH oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NADH oxidase

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