SMTL ID : 6hk1.2 (1 other biounit)

Crystal structure of the Thiazole synthase from Methanothermococcus thermolithotrophicus co-crystallized with Tb-Xo4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-octamer

Ligands

52 x TB: TERBIUM(III) ION(Non-covalent)(Non-functional Binders)

TB.1: 1 residues within 4Å: Chain A: D.177 Ligand excluded by PLIP TB.2: 1 residues within 4Å: Chain A: E.29 Ligand excluded by PLIP TB.3: 1 residues within 4Å: Chain A: E.51 Ligand excluded by PLIP TB.4: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.7: 1 residues within 4Å: Chain B: E.29 Ligand excluded by PLIP TB.8: 1 residues within 4Å: Chain B: E.51 Ligand excluded by PLIP TB.9: 1 residues within 4Å: Chain B: D.177 Ligand excluded by PLIP TB.10: 1 residues within 4Å: Chain B: K.6 Ligand excluded by PLIP TB.11: 1 residues within 4Å: Chain B: K.205 Ligand excluded by PLIP TB.12: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.14: 1 residues within 4Å: Chain B: K.97 Ligand excluded by PLIP TB.17: 1 residues within 4Å: Chain C: E.29 Ligand excluded by PLIP TB.18: 1 residues within 4Å: Chain C: K.4 Ligand excluded by PLIP TB.19: 1 residues within 4Å: Chain C: E.51 Ligand excluded by PLIP TB.20: 1 residues within 4Å: Chain C: D.177 Ligand excluded by PLIP TB.21: 1 residues within 4Å: Chain C: D.2 Ligand excluded by PLIP TB.22: 1 residues within 4Å: Chain C: E.82 Ligand excluded by PLIP TB.23: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.25: 1 residues within 4Å: Chain D: D.177 Ligand excluded by PLIP TB.26: 1 residues within 4Å: Chain D: E.29 Ligand excluded by PLIP TB.27: 1 residues within 4Å: Chain D: E.51 Ligand excluded by PLIP TB.28: 1 residues within 4Å: Chain D: K.6 Ligand excluded by PLIP TB.29: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.30: 1 residues within 4Å: Chain D: K.97 Ligand excluded by PLIP TB.34: 1 residues within 4Å: Chain E: D.177 Ligand excluded by PLIP TB.35: 1 residues within 4Å: Chain E: E.29 Ligand excluded by PLIP TB.36: 1 residues within 4Å: Chain E: E.51 Ligand excluded by PLIP TB.37: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.38: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.40: 1 residues within 4Å: Chain F: E.29 Ligand excluded by PLIP TB.41: 1 residues within 4Å: Chain F: E.51 Ligand excluded by PLIP TB.42: 1 residues within 4Å: Chain F: D.177 Ligand excluded by PLIP TB.43: 1 residues within 4Å: Chain F: K.6 Ligand excluded by PLIP TB.44: 1 residues within 4Å: Chain F: K.205 Ligand excluded by PLIP TB.45: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.46: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.47: 1 residues within 4Å: Chain F: K.97 Ligand excluded by PLIP TB.50: 1 residues within 4Å: Chain G: E.29 Ligand excluded by PLIP TB.51: 1 residues within 4Å: Chain G: K.4 Ligand excluded by PLIP TB.52: 1 residues within 4Å: Chain G: E.51 Ligand excluded by PLIP TB.53: 1 residues within 4Å: Chain G: D.177 Ligand excluded by PLIP TB.54: 1 residues within 4Å: Chain G: D.2 Ligand excluded by PLIP TB.55: 1 residues within 4Å: Chain G: E.82 Ligand excluded by PLIP TB.56: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.58: 1 residues within 4Å: Chain H: D.177 Ligand excluded by PLIP TB.59: 1 residues within 4Å: Chain H: E.29 Ligand excluded by PLIP TB.60: 1 residues within 4Å: Chain H: E.51 Ligand excluded by PLIP TB.61: 1 residues within 4Å: Chain H: K.6 Ligand excluded by PLIP TB.62: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.63: 1 residues within 4Å: Chain H: K.97 Ligand excluded by PLIP

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.6: 27 residues within 4Å: Chain A: V.35, G.36, G.37, G.38, P.39, S.40, L.58, E.59, R.60, H.61, G.66, G.67, V.131, A.132, V.133, A.173, T.174, G.175, S.179, G.225, M.226, M.237, G.238, F.241, M.244 Chain D: H.159, D.161 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:G.37, A:S.40, A:S.40, A:S.40, A:R.60, A:R.60, A:G.66, A:G.67, A:V.133, A:V.133, A:S.179, A:M.226, A:G.238 Water bridges: A:G.38, A:G.41, A:G.175, A:G.175 Salt bridges: D:H.159 48F.15: 27 residues within 4Å: Chain B: V.35, G.36, G.37, G.38, P.39, S.40, L.58, E.59, R.60, H.61, G.66, G.67, V.131, A.132, V.133, A.173, T.174, G.175, S.179, G.225, M.226, M.237, G.238, F.241, M.244 Chain C: H.159, D.161 20 PLIP interactions: 19 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:G.37, B:S.40, B:S.40, B:S.40, B:R.60, B:G.67, B:V.133, B:V.133, B:S.179, B:M.226, B:M.237, B:G.238 Water bridges: B:G.38, B:G.41, B:R.60, B:G.175, B:A.227 pi-Cation interactions: B:R.60, B:R.60 Salt bridges: C:H.159 48F.24: 27 residues within 4Å: Chain C: V.35, G.36, G.37, G.38, P.39, S.40, L.58, E.59, R.60, H.61, G.66, G.67, V.131, A.132, V.133, A.173, T.174, G.175, S.179, G.225, M.226, M.237, G.238, F.241, M.244 Chain F: H.159, D.161 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:G.37, C:S.40, C:S.40, C:S.40, C:R.60, C:R.60, C:G.67, C:V.133, C:V.133, C:S.179, C:M.226, C:M.237, C:G.238 Water bridges: C:G.175, C:G.175 Salt bridges: F:H.159 48F.31: 27 residues within 4Å: Chain D: V.35, G.36, G.37, G.38, P.39, S.40, L.58, E.59, R.60, H.61, G.66, G.67, V.131, A.132, V.133, A.173, T.174, G.175, S.179, G.225, M.226, M.237, G.238, F.241, M.244 Chain E: H.159, D.161 20 PLIP interactions: 19 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:G.37, D:S.40, D:S.40, D:S.40, D:R.60, D:R.60, D:H.61, D:G.67, D:V.133, D:V.133, D:S.179, D:M.226, D:M.237, D:G.238 Water bridges: D:G.38, D:G.41, D:H.61, D:G.175, D:G.175 Salt bridges: E:H.159 48F.39: 27 residues within 4Å: Chain E: V.35, G.36, G.37, G.38, P.39, S.40, L.58, E.59, R.60, H.61, G.66, G.67, V.131, A.132, V.133, A.173, T.174, G.175, S.179, G.225, M.226, M.237, G.238, F.241, M.244 Chain H: H.159, D.161 18 PLIP interactions: 17 interactions with chain E, 1 interactions with chain H Hydrogen bonds: E:G.37, E:S.40, E:S.40, E:S.40, E:R.60, E:R.60, E:G.66, E:G.67, E:V.133, E:V.133, E:S.179, E:M.226, E:G.238 Water bridges: E:G.38, E:G.41, E:G.175, E:G.175 Salt bridges: H:H.159 48F.48: 27 residues within 4Å: Chain F: V.35, G.36, G.37, G.38, P.39, S.40, L.58, E.59, R.60, H.61, G.66, G.67, V.131, A.132, V.133, A.173, T.174, G.175, S.179, G.225, M.226, M.237, G.238, F.241, M.244 Chain G: H.159, D.161 21 PLIP interactions: 20 interactions with chain F, 1 interactions with chain G Hydrogen bonds: F:G.37, F:S.40, F:S.40, F:S.40, F:R.60, F:H.61, F:G.67, F:V.133, F:V.133, F:S.179, F:M.226, F:M.237, F:G.238 Water bridges: F:G.38, F:G.41, F:R.60, F:G.175, F:A.227 pi-Cation interactions: F:R.60, F:R.60 Salt bridges: G:H.159 48F.57: 27 residues within 4Å: Chain B: H.159, D.161 Chain G: V.35, G.36, G.37, G.38, P.39, S.40, L.58, E.59, R.60, H.61, G.66, G.67, V.131, A.132, V.133, A.173, T.174, G.175, S.179, G.225, M.226, M.237, G.238, F.241, M.244 17 PLIP interactions: 16 interactions with chain G, 1 interactions with chain B Hydrogen bonds: G:G.37, G:S.40, G:S.40, G:S.40, G:R.60, G:R.60, G:H.61, G:G.67, G:V.133, G:V.133, G:S.179, G:M.226, G:M.237, G:G.238 Water bridges: G:G.175, G:G.175 Salt bridges: B:H.159 48F.64: 27 residues within 4Å: Chain A: H.159, D.161 Chain H: V.35, G.36, G.37, G.38, P.39, S.40, L.58, E.59, R.60, H.61, G.66, G.67, V.131, A.132, V.133, A.173, T.174, G.175, S.179, G.225, M.226, M.237, G.238, F.241, M.244 19 PLIP interactions: 18 interactions with chain H, 1 interactions with chain A Hydrogen bonds: H:G.37, H:S.40, H:S.40, H:S.40, H:R.60, H:R.60, H:G.67, H:V.133, H:V.133, H:S.179, H:M.226, H:M.237, H:G.238 Water bridges: H:G.38, H:G.41, H:H.61, H:G.175, H:G.175 Salt bridges: A:H.159

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

PEG.16: 4 residues within 4Å: Chain B: E.216, V.217, Y.218, P.219 No protein-ligand interaction detected (PLIP) PEG.49: 4 residues within 4Å: Chain F: E.216, V.217, Y.218, P.219 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.32: 7 residues within 4Å: Chain D: M.23, D.26, V.27, K.54, V.55, G.124, K.126 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:M.23, D:D.26, D:G.124 GOL.65: 7 residues within 4Å: Chain H: M.23, D.26, V.27, K.54, V.55, G.124, K.126 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:M.23, H:G.124

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

PGE.33: 5 residues within 4Å: Chain D: D.141, E.216, V.217, Y.218, P.219 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.141 PGE.66: 5 residues within 4Å: Chain H: D.141, E.216, V.217, Y.218, P.219 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Engilberge, S. et al., Protein crystal structure determination with the crystallophore, a nucleating and phasing agent. J.Appl.Crystallogr. (2019)

Release Date

2019-06-19

Peptides

Thiazole synthase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

D
F

E
B

F
C

G
D

H
F

Thiazole synthase

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