SMTL ID : 4y4m.1

Thiazole synthase Thi4 from Methanocaldococcus jannaschii

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.71 Å

Oligo State

homo-octamer

Ligands

8 x 48F: [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R)-2,3,5-tris(oxidanyl)-4-oxidanylidene-pentyl] hydrogen phosphate(Non-covalent)

48F.1: 29 residues within 4Å: Chain A: V.65, G.66, A.67, G.68, P.69, S.70, L.88, E.89, R.90, H.91, G.96, G.97, I.159, V.160, V.161, A.201, T.202, G.203, S.207, I.208, G.252, M.253, M.264, G.265, I.267, F.268, M.271 Chain D: H.187, D.189 14 PLIP interactions: 1 interactions with chain D, 13 interactions with chain A Salt bridges: D:H.187 Hydrogen bonds: A:S.70, A:S.70, A:S.70, A:R.90, A:R.90, A:G.96, A:G.97, A:V.161, A:V.161, A:S.207, A:M.253, A:G.265 pi-Cation interactions: A:R.90 48F.3: 27 residues within 4Å: Chain B: V.65, G.66, G.68, P.69, S.70, L.88, E.89, R.90, H.91, G.96, G.97, I.159, V.160, V.161, A.201, T.202, G.203, S.207, I.208, G.252, M.253, M.264, G.265, F.268, M.271 Chain F: H.187, D.189 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:S.70, B:S.70, B:S.70, B:R.90, B:R.90, B:G.96, B:G.97, B:V.161, B:V.161, B:G.203, B:S.207, B:M.253, B:M.264, B:G.265 pi-Cation interactions: B:R.90 Salt bridges: F:H.187 48F.4: 27 residues within 4Å: Chain B: H.187, D.189 Chain C: V.65, G.66, G.68, P.69, S.70, L.88, E.89, R.90, H.91, G.96, G.97, I.159, V.160, V.161, A.201, T.202, G.203, S.207, I.208, G.252, M.253, M.264, G.265, F.268, M.271 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:S.70, C:S.70, C:S.70, C:R.90, C:R.90, C:G.96, C:G.97, C:V.161, C:V.161, C:G.203, C:S.207, C:M.253, C:M.264, C:G.265 pi-Cation interactions: C:R.90 48F.6: 28 residues within 4Å: Chain D: V.65, G.66, A.67, G.68, P.69, S.70, L.88, E.89, R.90, H.91, G.96, G.97, I.159, V.160, V.161, A.201, T.202, G.203, S.207, I.208, G.252, M.253, M.264, G.265, F.268, M.271 Chain E: H.187, D.189 15 PLIP interactions: 14 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:S.70, D:S.70, D:S.70, D:R.90, D:R.90, D:G.96, D:G.97, D:V.161, D:V.161, D:G.203, D:S.207, D:M.253, D:M.264, D:G.265 Salt bridges: E:H.187 48F.7: 28 residues within 4Å: Chain E: V.65, G.66, G.68, P.69, S.70, L.88, E.89, R.90, H.91, G.96, G.97, I.159, V.160, V.161, A.201, T.202, G.203, S.207, I.208, G.252, M.253, R.263, M.264, G.265, F.268, M.271 Chain G: H.187, D.189 16 PLIP interactions: 15 interactions with chain E, 1 interactions with chain G Hydrogen bonds: E:S.70, E:S.70, E:S.70, E:R.90, E:R.90, E:G.96, E:G.97, E:V.161, E:V.161, E:G.203, E:S.207, E:M.253, E:M.264, E:G.265 pi-Cation interactions: E:R.90 Salt bridges: G:H.187 48F.8: 28 residues within 4Å: Chain F: V.65, G.66, G.68, P.69, S.70, L.88, E.89, R.90, H.91, G.96, G.97, I.159, V.160, V.161, A.201, T.202, G.203, S.207, I.208, G.252, M.253, M.264, G.265, I.267, F.268, M.271 Chain H: H.187, D.189 17 PLIP interactions: 1 interactions with chain H, 16 interactions with chain F Salt bridges: H:H.187 Hydrogen bonds: F:S.70, F:S.70, F:S.70, F:R.90, F:R.90, F:G.96, F:G.97, F:V.161, F:V.161, F:S.207, F:M.253, F:G.265 Water bridges: F:G.68, F:G.71, F:G.203, F:G.203 48F.10: 28 residues within 4Å: Chain A: H.187, D.189 Chain G: V.65, G.66, G.68, P.69, S.70, L.88, E.89, R.90, H.91, G.96, G.97, I.159, V.160, V.161, A.201, T.202, G.203, S.207, I.208, G.252, M.253, M.264, G.265, I.267, F.268, M.271 17 PLIP interactions: 16 interactions with chain G, 1 interactions with chain A Hydrogen bonds: G:S.70, G:S.70, G:S.70, G:R.90, G:R.90, G:G.96, G:G.97, G:V.161, G:V.161, G:G.203, G:S.207, G:M.253, G:G.265 Water bridges: G:G.68, G:G.71, G:A.254 Salt bridges: A:H.187 48F.12: 28 residues within 4Å: Chain C: H.187, D.189 Chain H: V.65, G.66, G.68, P.69, S.70, L.88, E.89, R.90, H.91, G.96, G.97, I.159, V.160, V.161, A.201, T.202, G.203, S.207, I.208, G.252, M.253, M.264, G.265, I.267, F.268, M.271 14 PLIP interactions: 1 interactions with chain C, 13 interactions with chain H Salt bridges: C:H.187 Hydrogen bonds: H:S.70, H:S.70, H:S.70, H:R.90, H:R.90, H:G.96, H:G.97, H:V.161, H:V.161, H:S.207, H:M.253, H:G.265 pi-Cation interactions: H:R.90

5 x NHE: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID(Non-covalent)

NHE.2: 7 residues within 4Å: Chain A: V.209, D.221, P.223, V.244, S.258, H.259, G.260 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.209, A:V.244 NHE.5: 6 residues within 4Å: Chain C: A.220, D.221, V.222, V.244, S.258, H.259 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.221 NHE.9: 6 residues within 4Å: Chain F: A.220, D.221, P.223, V.244, S.258, H.259 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:A.220, F:V.244 NHE.11: 6 residues within 4Å: Chain G: A.220, D.221, P.223, V.244, S.258, H.259 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:A.220, G:V.244 NHE.13: 8 residues within 4Å: Chain H: V.209, A.220, D.221, P.223, V.244, S.258, H.259, G.260 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:V.209, H:A.220, H:V.244

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, X. et al., Structural Basis for Iron-Mediated Sulfur Transfer in Archael and Yeast Thiazole Synthases. Biochemistry (2016)

Release Date

2016-03-09

Peptides

Putative ribose 1,5-bisphosphate isomerase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Putative ribose 1,5-bisphosphate isomerase