SMTL ID : 5mit.1

Crystal Structure of Lactococcus lactis Thioredoxin Reductase Exposed to Visible Light (240 min)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 33 residues within 4Å: Chain A: G.31, G.33, P.34, A.35, E.54, R.55, G.59, G.60, Q.61, N.64, T.65, I.68, N.70, G.100, F.101, V.102, A.129, T.130, G.131, A.132, S.174, E.177, E.178, V.262, F.265, G.295, D.296, R.303, Q.304, I.305, A.308 Chain B: Y.42 Ligands: NAP.2 32 PLIP interactions: 31 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.65, A:E.178 Hydrogen bonds: A:G.33, A:A.35, A:G.36, A:R.55, A:G.59, A:G.60, A:Q.61, A:N.70, A:N.70, A:V.102, A:V.102, A:A.132, A:D.296, A:R.303, A:Q.304, A:I.305, B:Y.42 Water bridges: A:E.54, A:R.55, A:Q.61, A:Q.61, A:T.65, A:E.69, A:N.70, A:G.131, A:F.265, A:V.297, A:Q.304, A:T.306 pi-Cation interactions: A:R.55 FAD.7: 33 residues within 4Å: Chain A: Y.42 Chain B: G.31, G.33, P.34, A.35, E.54, R.55, G.59, G.60, Q.61, N.64, T.65, I.68, N.70, G.100, F.101, V.102, A.129, T.130, G.131, A.132, S.174, E.177, E.178, V.262, F.265, G.295, D.296, R.303, Q.304, I.305, A.308 Ligands: NAP.8 34 PLIP interactions: 33 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.65, B:E.178 Hydrogen bonds: B:G.33, B:A.35, B:G.36, B:R.55, B:G.59, B:G.60, B:Q.61, B:T.65, B:N.70, B:N.70, B:V.102, B:V.102, B:A.132, B:D.296, B:R.303, B:Q.304, B:I.305, A:Y.42 Water bridges: B:E.54, B:R.55, B:Q.61, B:Q.61, B:T.65, B:E.69, B:N.70, B:G.131, B:F.265, B:D.296, B:V.297, B:Q.304, B:T.306 pi-Cation interactions: B:R.55

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

NAP.2: 24 residues within 4Å: Chain A: N.70, I.169, G.170, G.171, G.172, D.173, S.174, E.177, M.192, H.193, R.194, R.195, R.199, S.220, V.221, P.222, Y.256, V.257, G.258, L.259, D.301, R.303, Q.304 Ligands: FAD.1 34 PLIP interactions: 33 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:D.173 Hydrogen bonds: A:N.70, A:G.171, A:G.171, A:S.174, A:S.174, A:E.177, A:R.194, A:D.301, A:R.303, A:Q.304, B:R.45 Water bridges: A:G.172, A:D.173, A:D.173, A:A.175, A:E.177, A:E.177, A:E.177, A:R.194, A:R.194, A:R.194, A:R.195, A:R.199, A:G.258, A:G.258, A:L.259, A:L.259, A:R.303 Salt bridges: A:H.193, A:R.194, A:R.195, A:R.199 pi-Cation interactions: A:R.194 NAP.8: 24 residues within 4Å: Chain B: N.70, I.169, G.170, G.171, G.172, D.173, S.174, E.177, M.192, H.193, R.194, R.195, R.199, S.220, V.221, P.222, Y.256, V.257, G.258, L.259, D.301, R.303, Q.304 Ligands: FAD.7 33 PLIP interactions: 32 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:D.173 Hydrogen bonds: B:N.70, B:G.171, B:G.171, B:D.173, B:S.174, B:S.174, B:E.177, B:H.193, B:R.194, B:D.301, B:R.303, B:Q.304, A:R.45 Water bridges: B:G.172, B:D.173, B:D.173, B:A.175, B:R.194, B:R.194, B:R.194, B:R.195, B:R.199, B:G.258, B:G.258, B:L.259, B:L.259, B:R.303 Salt bridges: B:H.193, B:R.194, B:R.195, B:R.199 pi-Cation interactions: B:R.194

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 8 residues within 4Å: Chain A: S.32, L.52, E.54, G.56, P.58, N.97, A.98, Y.99 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.32, A:G.56, A:A.98 PEG.4: 4 residues within 4Å: Chain A: I.279, D.281, R.285, T.286 No protein-ligand interaction detected (PLIP) PEG.9: 8 residues within 4Å: Chain B: S.32, L.52, E.54, G.56, P.58, N.97, A.98, Y.99 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.32, B:G.56, B:A.98 PEG.10: 4 residues within 4Å: Chain B: I.279, D.281, R.285, T.286 No protein-ligand interaction detected (PLIP)

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 5 residues within 4Å: Chain A: P.140, G.141, E.142, E.143, E.144 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.141, A:E.143, A:E.144 Water bridges: A:E.142, A:E.142 SO4.6: 2 residues within 4Å: Chain A: R.135, R.194 9 PLIP interactions: 9 interactions with chain A Water bridges: A:R.135, A:R.135, A:R.135, A:R.135, A:R.135, A:R.194, A:R.194 Salt bridges: A:R.135, A:R.194 SO4.11: 5 residues within 4Å: Chain B: P.140, G.141, E.142, E.143, E.144 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.141, B:E.143, B:E.144 Water bridges: B:E.142, B:E.142 SO4.12: 2 residues within 4Å: Chain B: R.135, R.194 9 PLIP interactions: 9 interactions with chain B Water bridges: B:R.135, B:R.135, B:R.135, B:R.135, B:R.135, B:R.194, B:R.194 Salt bridges: B:R.135, B:R.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Skjoldager, N. et al., The structure of Lactococcus lactis thioredoxin reductase reveals molecular features of photo-oxidative damage. Sci Rep (2017)

Release Date

2017-04-12

Peptides

Thioredoxin reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Thioredoxin reductase

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