SMTL ID : 6rvb.1 (1 other biounit)

NADH-dependent Coenzyme A Disulfide Reductase soaked with NADH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 35 residues within 4Å: Chain A: V.8, G.9, V.11, A.12, G.13, Y.33, E.34, K.35, S.36, A.43, C.44, P.47, H.79, E.80, V.81, A.112, T.113, G.114, A.115, L.133, R.134, I.160, A.279, G.280, D.281, P.297, L.298, G.299, D.300, A.302 Chain B: Y.424, A.425, P.426 Ligands: NAD.2, COA.3 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.43, A:L.133, A:I.160 Hydrogen bonds: A:A.12, A:G.13, A:K.35, A:S.36, A:V.81, A:V.81, A:A.115, A:R.134, A:A.279, A:D.281, A:P.297, A:G.299, A:D.300, B:Y.424 FAD.4: 36 residues within 4Å: Chain A: Y.424, A.425, P.426 Chain B: V.8, G.9, V.11, A.12, G.13, Y.33, E.34, K.35, S.36, A.43, C.44, P.47, H.79, E.80, V.81, A.112, T.113, G.114, A.115, L.133, R.134, I.160, E.163, A.279, G.280, D.281, P.297, L.298, G.299, D.300, A.302 Ligands: NAD.5, COA.6 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.43, B:L.133, B:I.160 Hydrogen bonds: B:A.12, B:G.13, B:K.35, B:S.36, B:S.36, B:V.81, B:V.81, B:A.115, B:R.134, B:A.279, B:D.281, B:P.297, B:G.299, B:D.300, B:D.300, A:Y.424

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 22 residues within 4Å: Chain A: P.120, R.134, L.155, G.156, A.157, G.158, Y.159, I.160, E.163, L.178, E.179, A.180, H.187, A.240, T.241, G.242, I.243, P.297, L.298, I.328, F.329 Ligands: FAD.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.159, A:I.160 Hydrogen bonds: A:R.134, A:G.158, A:Y.159, A:I.160, A:I.160, A:A.180, A:G.242, A:I.328 Water bridges: A:G.156, A:H.187, A:A.240 Salt bridges: A:H.187 NAD.5: 23 residues within 4Å: Chain A: A.425 Chain B: P.120, R.134, L.155, G.156, A.157, G.158, Y.159, I.160, E.163, L.178, E.179, A.180, H.187, A.240, T.241, G.242, I.243, P.297, L.298, I.328, F.329 Ligands: FAD.4 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.159, B:I.160 Hydrogen bonds: B:R.134, B:G.158, B:Y.159, B:I.160, B:I.160, B:A.180, B:A.240, B:G.242, B:I.328 Salt bridges: B:H.187

2 x COA: COENZYME A(Non-covalent)

COA.3: 25 residues within 4Å: Chain A: V.11, A.12, A.15, S.16, A.19, K.20, R.23, S.40, Y.41, G.42, A.43, C.44, A.62, R.63, F.68, G.299, N.303, R.307 Chain B: Q.359, S.360, V.431, I.437, Q.441, A.442 Ligands: FAD.1 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:A.15, A:F.68 Hydrogen bonds: A:N.303, B:Q.359, B:Q.441, B:A.442 Salt bridges: A:K.20, A:R.23, A:R.23, A:R.23, A:R.63, A:R.63, A:R.307 Water bridges: B:Y.424 COA.6: 23 residues within 4Å: Chain A: I.358, Q.359, S.360, V.431, I.437, Q.441, A.442 Chain B: V.11, A.12, A.15, A.19, K.20, R.23, S.40, Y.41, C.44, A.62, R.63, F.68, G.299, N.303, R.307 Ligands: FAD.4 16 PLIP interactions: 11 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:A.15, B:F.68 Hydrogen bonds: B:N.303, B:N.303, A:Q.359, A:Q.359, A:I.437, A:Q.441, A:A.442 Salt bridges: B:K.20, B:R.23, B:R.23, B:R.23, B:R.63, B:R.63, B:R.307

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lencina, A.M. et al., Characterization and X-ray structure of the NADH-dependent coenzyme A disulfide reductase from Thermus thermophilus. Biochim Biophys Acta Bioenerg (2019)

Release Date

2019-09-25

Peptides

NADH oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NADH oxidase

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