SMTL ID : 7rk0.1

Crystal structure of Thermovibrio ammonificans THI4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

homo-octamer

Ligands

8 x FE: FE (III) ION(Non-covalent)

FE.1: 3 residues within 4Å: Chain A: H.175 Chain B: D.160 Ligands: 48H.2 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.160, A:H.175, H2O.1 FE.3: 3 residues within 4Å: Chain B: H.175 Chain G: D.160 Ligands: 48H.4 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain G Metal complexes: B:H.175, G:D.160 FE.5: 3 residues within 4Å: Chain C: H.175 Chain D: D.160 Ligands: 48H.6 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Metal complexes: C:H.175, D:D.160 FE.7: 3 residues within 4Å: Chain D: H.175 Chain E: D.160 Ligands: 48H.8 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Metal complexes: E:D.160, D:H.175 FE.9: 3 residues within 4Å: Chain E: H.175 Chain F: D.160 Ligands: 48H.10 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: E:H.175, F:D.160, H2O.2 FE.11: 3 residues within 4Å: Chain C: D.160 Chain F: H.175 Ligands: 48H.12 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain C Metal complexes: F:H.175, C:D.160 FE.13: 3 residues within 4Å: Chain G: H.175 Chain H: D.160 Ligands: 48H.14 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain G Metal complexes: H:D.160, G:H.175 FE.15: 3 residues within 4Å: Chain A: D.160 Chain H: H.175 Ligands: 48H.16 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain H Metal complexes: A:D.160, H:H.175

8 x 48H: 2-[(E)-[(4R)-5-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-4-oxidanyl-3-oxidanylidene-pentan-2-ylidene]amino]ethanoic acid(Non-covalent)

48H.2: 32 residues within 4Å: Chain A: V.32, G.33, G.35, P.36, S.37, F.55, E.56, R.57, R.58, G.63, G.64, V.126, T.127, A.128, A.172, T.173, G.174, H.175, S.178, L.204, G.228, M.229, R.239, M.240, G.241, V.243, F.244, M.247 Chain B: M.158, D.160, P.161 Ligands: FE.1 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:G.35, A:S.37, A:S.37, A:S.37, A:R.57, A:R.58, A:R.58, A:R.58, A:G.64, A:A.128, A:A.128, A:S.178, A:M.229, A:M.240, A:G.241, A:G.241 Water bridges: A:G.174 Salt bridges: A:H.175, A:R.239 48H.4: 33 residues within 4Å: Chain B: V.32, G.33, G.34, G.35, P.36, S.37, F.55, E.56, R.57, R.58, G.63, G.64, M.65, V.126, T.127, A.128, A.172, T.173, G.174, H.175, S.178, G.228, M.229, R.239, M.240, G.241, V.243, F.244, M.247 Chain G: M.158, D.160, P.161 Ligands: FE.3 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:G.34, B:S.37, B:S.37, B:S.37, B:R.57, B:R.58, B:G.64, B:A.128, B:A.128, B:S.178, B:M.229 Water bridges: B:G.174, B:G.174 Salt bridges: B:H.175, B:R.239 48H.6: 30 residues within 4Å: Chain C: V.32, G.33, G.35, P.36, S.37, F.55, E.56, R.57, R.58, G.63, G.64, V.126, T.127, A.128, A.172, T.173, G.174, H.175, S.178, G.228, M.229, R.239, M.240, G.241, V.243, F.244, M.247 Chain D: D.160, P.161 Ligands: FE.5 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:S.37, C:S.37, C:R.57, C:R.58, C:R.58, C:G.64, C:A.128, C:S.178, C:S.178, C:M.229, C:M.240, C:G.241 Water bridges: C:H.175 Salt bridges: C:H.175, C:R.239 48H.8: 31 residues within 4Å: Chain D: V.32, G.33, G.35, P.36, S.37, F.55, E.56, R.57, R.58, G.63, G.64, M.65, V.126, T.127, A.128, A.172, T.173, G.174, H.175, S.178, G.228, M.229, R.239, M.240, G.241, V.243, F.244, M.247 Chain E: M.158, D.160 Ligands: FE.7 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:S.37, D:S.37, D:R.57, D:R.58, D:G.63, D:G.64, D:A.128, D:S.178, D:S.178, D:M.229, D:M.240, D:G.241 Salt bridges: D:H.175, D:R.239 pi-Cation interactions: D:R.57 48H.10: 32 residues within 4Å: Chain E: V.32, G.33, G.35, P.36, S.37, F.55, E.56, R.57, R.58, G.63, G.64, V.126, T.127, A.128, A.172, T.173, G.174, H.175, S.178, L.204, G.228, M.229, R.239, M.240, G.241, V.243, F.244, M.247 Chain F: M.158, D.160, P.161 Ligands: FE.9 20 PLIP interactions: 20 interactions with chain E Hydrogen bonds: E:G.35, E:S.37, E:S.37, E:S.37, E:R.57, E:R.58, E:R.58, E:R.58, E:G.64, E:A.128, E:A.128, E:T.173, E:S.178, E:M.229, E:M.240, E:G.241, E:G.241 Water bridges: E:G.174 Salt bridges: E:H.175, E:R.239 48H.12: 33 residues within 4Å: Chain C: M.158, D.160, P.161 Chain F: V.32, G.33, G.34, G.35, P.36, S.37, F.55, E.56, R.57, R.58, G.63, G.64, M.65, V.126, T.127, A.128, A.172, T.173, G.174, H.175, S.178, G.228, M.229, R.239, M.240, G.241, V.243, F.244, M.247 Ligands: FE.11 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:G.34, F:S.37, F:S.37, F:S.37, F:R.57, F:R.58, F:G.63, F:G.64, F:A.128, F:A.128, F:S.178, F:M.229 Water bridges: F:G.174, F:G.174 Salt bridges: F:H.175, F:R.239 48H.14: 30 residues within 4Å: Chain G: V.32, G.33, G.35, P.36, S.37, F.55, E.56, R.57, R.58, G.63, G.64, V.126, T.127, A.128, A.172, T.173, G.174, H.175, S.178, G.228, M.229, R.239, M.240, G.241, V.243, F.244, M.247 Chain H: D.160, P.161 Ligands: FE.13 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:S.37, G:S.37, G:R.57, G:R.58, G:R.58, G:G.64, G:A.128, G:S.178, G:S.178, G:M.229, G:M.240, G:G.241 Water bridges: G:H.175 Salt bridges: G:H.175, G:R.239 48H.16: 31 residues within 4Å: Chain A: M.158, D.160 Chain H: V.32, G.33, G.35, P.36, S.37, F.55, E.56, R.57, R.58, G.63, G.64, M.65, V.126, T.127, A.128, A.172, T.173, G.174, H.175, S.178, G.228, M.229, R.239, M.240, G.241, V.243, F.244, M.247 Ligands: FE.15 17 PLIP interactions: 15 interactions with chain H, 2 interactions with chain A Hydrogen bonds: H:S.37, H:S.37, H:R.57, H:R.58, H:G.63, H:G.64, H:A.128, H:S.178, H:S.178, H:M.229, H:M.240, H:G.241, A:D.160, A:D.160 Salt bridges: H:H.175, H:R.239 pi-Cation interactions: H:R.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joshi, J. et al., Structure and function of aerotolerant, multiple-turnover THI4 thiazole synthases. Biochem.J. (2021)

Release Date

2021-09-01

Peptides

Thiamine thiazole synthase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

Thiamine thiazole synthase