SMTL ID : 5vt3.1

High resolution structure of thioredoxin-disulfide reductase from Vibrio vulnificus CMCP6 in complex with NADP and FAD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 22 residues within 4Å: Chain A: N.55, L.123, G.156, G.157, G.158, N.159, T.160, E.163, H.179, R.180, R.181, R.185, E.187, L.190, A.245, I.246, G.247, H.248, Y.295, R.296, Q.297 Ligands: FAD.2 36 PLIP interactions: 35 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:N.159 Hydrogen bonds: A:N.55, A:G.157, A:G.157, A:N.159, A:T.160, A:T.160, A:E.163, A:R.180, A:R.180, A:R.296, A:Q.297 Water bridges: A:K.121, A:G.158, A:N.159, A:T.160, A:A.161, A:R.185, A:R.185, A:A.245, A:R.296, A:R.296, A:R.296, A:R.296, A:R.296, A:R.296, A:R.296, B:R.30 Salt bridges: A:H.179, A:R.180, A:R.181, A:R.185, A:H.248, A:R.296 pi-Cation interactions: A:R.180, A:R.180 NAP.7: 21 residues within 4Å: Chain B: N.55, K.121, L.123, G.156, G.157, G.158, N.159, T.160, E.163, H.179, R.180, R.181, R.185, A.245, I.246, G.247, H.248, Y.295, R.296, Q.297 Ligands: FAD.8 32 PLIP interactions: 31 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:N.159 Hydrogen bonds: B:N.55, B:K.121, B:G.157, B:G.157, B:N.159, B:T.160, B:T.160, B:R.180, B:R.180, B:E.187, B:R.296, B:R.296, B:Q.297 Water bridges: B:G.158, B:N.159, B:T.160, B:A.161, B:R.185, B:E.187, B:A.245, B:H.248, B:Y.295, B:R.296, A:R.30 Salt bridges: B:H.179, B:R.180, B:R.181, B:R.185, B:R.296 pi-Cation interactions: B:R.180, B:R.180

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

FAD.2: 35 residues within 4Å: Chain A: G.16, S.17, G.18, P.19, A.20, T.39, G.40, M.41, Q.42, G.45, Q.46, L.47, T.49, T.50, E.52, N.55, H.87, I.88, S.115, T.116, G.117, A.118, E.163, H.248, N.251, I.254, G.288, D.289, R.296, Q.297, A.298, S.301 Chain B: Y.27 Ligands: NAP.1, K.3 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:T.50 Hydrogen bonds: A:S.17, A:G.18, A:A.20, A:Q.42, A:Q.42, A:Q.46, A:Q.46, A:N.55, A:N.55, A:I.88, A:I.88, A:A.118, A:D.289, A:R.296, A:A.298, A:S.301 Water bridges: A:G.21, A:M.41, A:M.41, A:Q.42, A:L.47, A:L.47, A:E.54, A:N.55, A:G.117, A:A.118, A:V.290, A:I.299 FAD.8: 36 residues within 4Å: Chain A: Y.27 Chain B: G.16, S.17, G.18, P.19, A.20, T.39, G.40, M.41, Q.42, G.45, Q.46, L.47, T.49, T.50, E.52, V.53, N.55, H.87, I.88, S.115, T.116, G.117, A.118, E.163, H.248, N.251, I.254, G.288, D.289, R.296, Q.297, A.298, S.301 Ligands: NAP.7, K.9 28 PLIP interactions: 27 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Q.46 Hydrogen bonds: B:S.17, B:G.18, B:A.20, B:Q.42, B:Q.42, B:Q.46, B:Q.46, B:L.47, B:N.55, B:N.55, B:I.88, B:I.88, B:A.118, B:D.289, B:R.296, B:A.298, B:S.301, A:Y.27 Water bridges: B:G.21, B:M.41, B:Q.42, B:E.54, B:N.55, B:G.117, B:A.118, B:V.290, B:I.299

2 x K: POTASSIUM ION(Non-covalent)

K.3: 4 residues within 4Å: Chain A: T.50, E.52, E.163 Ligands: FAD.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:T.50, A:E.52, A:E.163, A:E.163 K.9: 4 residues within 4Å: Chain B: T.50, E.52, E.163 Ligands: FAD.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.50, B:E.52, B:E.163

2 x CAC: CACODYLATE ION(Non-covalent)

CAC.4: 5 residues within 4Å: Chain A: D.260, L.267, V.268, T.279, S.280 No protein-ligand interaction detected (PLIP) CAC.10: 5 residues within 4Å: Chain B: D.260, L.267, K.269, T.279, S.280 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.260, B:L.267

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: G.271 Chain B: S.270, A.276, M.291 Ligands: GOL.6 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.276 Water bridges: A:G.271 GOL.6: 6 residues within 4Å: Chain A: S.270, A.276, M.291 Chain B: S.270, G.271 Ligands: GOL.5 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.271, A:A.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chang, C. et al., High resolution structure of thioredoxin-disulfide reductase from Vibrio vulnificus CMCP6 in complex with NADP and FAD. To Be Published

Release Date

2017-05-31

Peptides

Thioredoxin reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thioredoxin reductase