SMTL ID : 6xtf.1

Crystal structure a Thioredoxin Reductase from Gloeobacter violaceus bound to its electron donor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

hetero-2-2-mer

Ligands

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

FAD.1: 43 residues within 4Å: Chain A: V.14, G.15, G.16, G.17, P.18, A.19, G.20, L.37, D.38, K.39, N.40, P.41, A.43, G.44, A.45, L.46, I.48, T.49, K.51, I.52, N.54, A.85, Q.86, V.87, A.114, T.115, G.116, A.117, M.118, I.247, F.250, G.280, D.281, I.282, K.288, Q.289, A.290, V.291, A.293 Chain C: S.42, C.43, A.47, C.48 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:T.49 Hydrogen bonds: A:G.16, A:G.17, A:A.19, A:K.39, A:N.40, A:A.45, A:L.46, A:T.49, A:N.54, A:N.54, A:V.87, A:V.87, A:D.281, A:Q.289, A:A.290 Water bridges: A:A.43, A:G.44, A:A.53, A:N.54, A:Q.86, A:A.117, A:A.117, A:I.282, A:V.291 FAD.15: 42 residues within 4Å: Chain B: V.14, G.15, G.16, G.17, P.18, A.19, G.20, L.37, D.38, K.39, N.40, P.41, A.43, G.44, A.45, L.46, I.48, T.49, I.52, N.54, L.68, A.85, Q.86, V.87, A.114, T.115, G.116, A.117, M.118, I.247, F.250, G.280, D.281, I.282, K.288, Q.289, A.290, V.291, A.293 Chain D: S.42, C.43 Ligands: PEG.24 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:T.49 Hydrogen bonds: B:G.16, B:G.16, B:G.17, B:A.19, B:K.39, B:K.39, B:N.40, B:A.45, B:L.46, B:T.49, B:N.54, B:N.54, B:V.87, B:V.87, B:D.281, B:Q.289, B:A.290 Water bridges: B:G.44, B:N.54, B:Q.86, B:A.117, B:V.291

12 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 7 residues within 4Å: Chain A: E.69, D.73 Chain B: Q.165, T.168, K.169, H.195 Ligands: PEG.14 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.169 Water bridges: B:E.191 ACT.4: 3 residues within 4Å: Chain A: D.10, K.33, R.109 No protein-ligand interaction detected (PLIP) ACT.5: 4 residues within 4Å: Chain A: T.217, A.218, E.231, L.233 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.217 ACT.10: 8 residues within 4Å: Chain A: G.119, I.121, K.245, P.246, I.247, T.248, D.249 Ligands: ACT.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.248, A:D.249 ACT.11: 5 residues within 4Å: Chain A: R.120, Y.137, I.247, D.249 Ligands: ACT.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.249 Water bridges: A:R.120 ACT.12: 2 residues within 4Å: Chain A: A.252, G.253 No protein-ligand interaction detected (PLIP) ACT.13: 4 residues within 4Å: Chain A: Q.6, F.7, D.8, K.33 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.6, A:Q.6, A:F.7, A:D.8 Salt bridges: A:K.33 ACT.18: 8 residues within 4Å: Chain B: W.201, T.204, V.221, R.222, H.223, D.228, S.229, Q.230 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.228 Water bridges: B:H.223 Salt bridges: B:H.223 ACT.20: 4 residues within 4Å: Chain B: D.8, F.9, D.10, R.109 No protein-ligand interaction detected (PLIP) ACT.21: 6 residues within 4Å: Chain B: Y.88, Y.100, T.101, P.102, G.104, I.105 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.88 ACT.25: 2 residues within 4Å: Chain B: N.148, R.149 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.148 Salt bridges: B:R.149 ACT.31: 3 residues within 4Å: Chain D: D.97, E.98, Y.100 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.97

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

PEG.3: 5 residues within 4Å: Chain A: D.91, K.98, Y.100, I.105, T.107 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.91, A:K.98, A:Y.100 PEG.7: 6 residues within 4Å: Chain A: P.95, V.96, R.109, F.307, L.308, S.310 No protein-ligand interaction detected (PLIP) PEG.14: 7 residues within 4Å: Chain A: D.73, V.76, E.77 Chain B: E.162, Q.165, E.191 Ligands: ACT.2 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.191 PEG.17: 6 residues within 4Å: Chain B: P.95, V.96, R.109, F.307, L.308, S.310 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.310 PEG.22: 9 residues within 4Å: Chain B: G.132, R.133, G.134, F.145, Y.146, R.149, A.214, G.215, E.235 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.235 PEG.24: 9 residues within 4Å: Chain B: G.119, R.120, K.245, P.246, I.247, T.248, D.249, F.250 Ligands: FAD.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.248, B:D.249, B:F.250 PEG.27: 8 residues within 4Å: Chain A: S.244, K.245 Chain C: Q.65, S.66, F.67, L.68, D.69 Ligands: PEG.29 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:S.244, A:K.245 Water bridges: C:Q.65, C:Q.65, C:S.66, C:F.67 PEG.28: 5 residues within 4Å: Chain C: D.38, L.39, P.40, F.41, T.50 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.38, C:F.41 PEG.29: 6 residues within 4Å: Chain C: Q.65, L.68, D.69, D.70, I.73 Ligands: PEG.27 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.70 Water bridges: C:Q.65 PEG.30: 7 residues within 4Å: Chain C: D.71, Q.72, A.75, Y.77, E.98, L.99, Y.100 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.100 Water bridges: C:D.71 PEG.33: 6 residues within 4Å: Chain D: D.71, Q.72, A.75, Y.77, E.98, L.99 No protein-ligand interaction detected (PLIP)

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.6: 17 residues within 4Å: Chain A: R.120, I.124, V.154, G.155, L.156, I.177, P.179, K.180, T.204, R.205, L.206, L.241 Chain C: Y.27, R.44, A.45, D.64, V.82 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.206 Water bridges: A:R.120 PG4.16: 3 residues within 4Å: Chain B: D.65, H.66, E.69 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.69 PG4.19: 5 residues within 4Å: Chain B: V.265, D.266, E.267, M.269, R.283 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.265

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.8: 2 residues within 4Å: Chain A: K.312, A.313 No protein-ligand interaction detected (PLIP) PGE.9: 3 residues within 4Å: Chain A: E.256, W.264, S.272 No protein-ligand interaction detected (PLIP) PGE.23: 3 residues within 4Å: Chain B: E.256, W.264, S.272 No protein-ligand interaction detected (PLIP)

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

FES.26: 13 residues within 4Å: Chain C: F.41, S.42, C.43, R.44, A.45, G.46, A.47, C.48, S.49, T.50, C.51, L.79, C.81 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.43, C:C.48, C:C.51, C:C.81 FES.32: 12 residues within 4Å: Chain D: F.41, S.42, C.43, R.44, A.45, G.46, A.47, C.48, T.50, C.51, L.79, C.81 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.43, D:C.48, D:C.51, D:C.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Buey, R.M. et al., Unexpected diversity of ferredoxin-dependent thioredoxin reductases in cyanobacteria. Plant Physiol. (2021)

Release Date

2021-07-28

Peptides

Thioredoxin reductase: AB
Ferredoxin: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Thioredoxin reductase

Ferredoxin

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