SMTL ID : 4y4n.1

Thiazole synthase Thi4 from Methanococcus igneus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-octamer

Ligands

8 x FE2: FE (II) ION(Non-covalent)

FE2.1: 3 residues within 4Å: Chain A: H.199 Chain C: D.184 Ligands: 48H.2 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:D.184, A:H.199, H2O.1 FE2.3: 3 residues within 4Å: Chain A: D.184 Chain H: H.199 Ligands: 48H.4 3 PLIP interactions: 1 interactions with chain H, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: H:H.199, A:D.184, H2O.1 FE2.5: 3 residues within 4Å: Chain B: H.199 Chain D: D.184 Ligands: 48H.6 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: B:H.199, D:D.184, H2O.4 FE2.7: 3 residues within 4Å: Chain B: D.184 Chain G: H.199 Ligands: 48H.8 3 PLIP interactions: 1 interactions with chain G, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: G:H.199, B:D.184, H2O.3 FE2.9: 3 residues within 4Å: Chain C: H.199 Chain F: D.184 Ligands: 48H.10 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: F:D.184, C:H.199, H2O.6 FE2.11: 3 residues within 4Å: Chain D: H.199 Chain E: D.184 Ligands: 48H.12 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: E:D.184, D:H.199, H2O.5 FE2.13: 3 residues within 4Å: Chain E: H.199 Chain G: D.184 Ligands: 48H.14 3 PLIP interactions: 1 interactions with chain G, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: G:D.184, E:H.199, H2O.7 FE2.15: 3 residues within 4Å: Chain F: H.199 Chain H: D.184 Ligands: 48H.16 3 PLIP interactions: 1 interactions with chain H, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: H:D.184, F:H.199, H2O.8

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: 29 residues within 4Å: Chain A: V.58, G.59, G.61, P.62, S.63, L.81, E.82, R.83, H.84, G.89, G.90, I.154, V.155, V.156, A.196, T.197, G.198, H.199, S.202, M.224, G.248, M.249, R.259, M.260, G.261, F.264, M.267 Chain C: D.184 Ligands: FE2.1 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:F.264 Hydrogen bonds: A:S.63, A:S.63, A:S.63, A:R.83, A:R.83, A:H.84, A:G.90, A:V.156, A:V.156, A:G.198, A:S.202, A:M.249, A:M.260, A:G.261 Water bridges: A:G.61, A:G.64, A:G.89, A:A.250 Salt bridges: A:H.199, A:R.259 pi-Cation interactions: A:R.83 48H.4: 30 residues within 4Å: Chain A: D.184, P.185 Chain H: V.58, G.59, G.61, P.62, S.63, L.81, E.82, R.83, H.84, G.89, G.90, I.154, V.155, V.156, A.196, T.197, G.198, H.199, S.202, M.224, G.248, M.249, R.259, M.260, G.261, F.264, M.267 Ligands: FE2.3 22 PLIP interactions: 22 interactions with chain H Hydrophobic interactions: H:F.264 Hydrogen bonds: H:S.63, H:S.63, H:R.83, H:R.83, H:H.84, H:G.90, H:V.156, H:V.156, H:A.196, H:S.202, H:M.249, H:M.260, H:G.261 Water bridges: H:G.61, H:G.64, H:G.198, H:G.198, H:R.259 Salt bridges: H:H.199, H:R.259 pi-Cation interactions: H:R.83 48H.6: 29 residues within 4Å: Chain B: V.58, G.59, G.61, P.62, S.63, L.81, E.82, R.83, H.84, G.89, G.90, I.154, V.155, V.156, A.196, T.197, G.198, H.199, S.202, M.224, G.248, M.249, R.259, M.260, G.261, F.264, M.267 Chain D: D.184 Ligands: FE2.5 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:F.264 Hydrogen bonds: B:S.63, B:S.63, B:S.63, B:R.83, B:R.83, B:H.84, B:G.90, B:V.156, B:V.156, B:S.202, B:M.249, B:M.260, B:G.261 Water bridges: B:G.61, B:G.64, B:G.89, B:G.198, B:G.198, B:R.259 Salt bridges: B:H.199, B:R.259 pi-Cation interactions: B:R.83, B:R.83 48H.8: 30 residues within 4Å: Chain B: D.184, P.185 Chain G: V.58, G.59, G.61, P.62, S.63, L.81, E.82, R.83, H.84, G.89, G.90, I.154, V.155, V.156, A.196, T.197, G.198, H.199, S.202, M.224, G.248, M.249, R.259, M.260, G.261, F.264, M.267 Ligands: FE2.7 25 PLIP interactions: 25 interactions with chain G Hydrophobic interactions: G:F.264 Hydrogen bonds: G:S.63, G:S.63, G:S.63, G:R.83, G:R.83, G:H.84, G:G.90, G:V.156, G:V.156, G:G.198, G:S.202, G:M.249, G:M.260, G:G.261 Water bridges: G:G.61, G:G.64, G:R.83, G:R.83, G:G.89, G:A.250 Salt bridges: G:H.199, G:R.259 pi-Cation interactions: G:R.83, G:R.83 48H.10: 29 residues within 4Å: Chain C: V.58, G.59, G.61, P.62, S.63, L.81, E.82, R.83, H.84, G.89, G.90, I.154, V.155, V.156, A.196, T.197, G.198, H.199, S.202, M.224, G.248, M.249, R.259, M.260, G.261, F.264, M.267 Chain F: D.184 Ligands: FE2.9 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:F.264 Hydrogen bonds: C:S.63, C:S.63, C:S.63, C:R.83, C:R.83, C:H.84, C:G.90, C:V.156, C:V.156, C:G.198, C:S.202, C:M.249, C:M.260, C:G.261 Water bridges: C:G.61, C:G.64, C:G.89, C:A.250 Salt bridges: C:H.199, C:R.259 pi-Cation interactions: C:R.83, C:R.83 48H.12: 29 residues within 4Å: Chain D: V.58, G.59, G.61, P.62, S.63, L.81, E.82, R.83, H.84, G.89, G.90, I.154, V.155, V.156, A.196, T.197, G.198, H.199, S.202, M.224, G.248, M.249, R.259, M.260, G.261, F.264, M.267 Chain E: D.184 Ligands: FE2.11 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:F.264 Hydrogen bonds: D:S.63, D:S.63, D:S.63, D:R.83, D:R.83, D:H.84, D:G.90, D:V.156, D:V.156, D:G.198, D:S.202, D:M.249, D:M.260, D:G.261 Water bridges: D:G.61, D:G.64, D:G.89, D:A.250 Salt bridges: D:H.199, D:R.259 pi-Cation interactions: D:R.83 48H.14: 30 residues within 4Å: Chain E: V.58, G.59, G.61, P.62, S.63, L.81, E.82, R.83, H.84, G.89, G.90, I.154, V.155, V.156, A.196, T.197, G.198, H.199, S.202, M.224, G.248, M.249, R.259, M.260, G.261, F.264, M.267 Chain G: D.184, P.185 Ligands: FE2.13 23 PLIP interactions: 23 interactions with chain E Hydrophobic interactions: E:F.264 Hydrogen bonds: E:S.63, E:S.63, E:S.63, E:R.83, E:R.83, E:H.84, E:G.90, E:V.156, E:V.156, E:S.202, E:M.249, E:M.260, E:G.261 Water bridges: E:G.61, E:G.64, E:G.89, E:G.198, E:G.198, E:R.259 Salt bridges: E:H.199, E:R.259 pi-Cation interactions: E:R.83 48H.16: 29 residues within 4Å: Chain F: V.58, G.59, G.61, P.62, S.63, L.81, E.82, R.83, H.84, G.89, G.90, I.154, V.155, V.156, A.196, T.197, G.198, H.199, S.202, M.224, G.248, M.249, R.259, M.260, G.261, F.264, M.267 Chain H: D.184 Ligands: FE2.15 23 PLIP interactions: 22 interactions with chain F, 1 interactions with chain H Hydrophobic interactions: F:F.264 Hydrogen bonds: F:S.63, F:S.63, F:S.63, F:R.83, F:R.83, F:H.84, F:G.90, F:V.156, F:V.156, F:G.198, F:S.202, F:M.249, F:M.260, F:G.261, H:D.184 Water bridges: F:G.61, F:G.64, F:G.89, F:A.250 Salt bridges: F:H.199, F:R.259 pi-Cation interactions: F:R.83

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