SMTL ID : 4ho8.5 (4 other biounits)

Crystal structure of glucose 1-phosphate thymidylyltransferase from Aneurinibacillus thermoaerophilus complexed with UDP-glucose and thymidine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

4 x UPG: URIDINE-5'-DIPHOSPHATE-GLUCOSE(Non-covalent)

UPG.1: 20 residues within 4Å: Chain A: L.6, G.8, G.9, K.23, Q.80, P.83, D.84, G.85, L.86, L.106, D.108, F.143, G.144, E.159, K.160, V.170, Y.174, R.192, W.221 Ligands: SO4.3 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:L.86 Hydrogen bonds: A:G.8, A:G.8, A:G.9, A:K.23, A:K.23, A:Q.80, A:Q.80, A:G.85, A:G.144, A:E.159, A:V.170, A:R.192 Water bridges: A:R.13, A:G.107, A:E.196, A:E.196, A:E.196 Salt bridges: A:K.160, A:K.160, A:R.192 UPG.6: 22 residues within 4Å: Chain B: L.6, G.8, G.9, R.13, K.23, Q.80, P.83, D.84, G.85, L.86, L.106, D.108, N.109, F.143, G.144, E.159, K.160, V.170, G.172, R.192, W.221 Ligands: SO4.8 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:G.8, B:R.13, B:K.23, B:K.23, B:Q.80, B:Q.80, B:G.85, B:N.109, B:G.144, B:E.159, B:V.170, B:R.192, B:R.192 Water bridges: B:G.107 Salt bridges: B:K.160, B:K.160, B:R.192 UPG.12: 21 residues within 4Å: Chain C: L.6, G.8, G.9, K.23, Q.80, P.83, D.84, G.85, L.86, L.106, D.108, N.109, F.143, G.144, E.159, K.160, V.170, G.172, R.192, W.221 Ligands: SO4.14 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:L.86 Hydrogen bonds: C:G.8, C:K.23, C:K.23, C:Q.80, C:Q.80, C:G.85, C:N.109, C:G.144, C:E.159, C:R.192, C:R.192 Water bridges: C:G.9, C:G.9, C:V.170, C:T.171 Salt bridges: C:K.160, C:K.160, C:R.192 UPG.18: 23 residues within 4Å: Chain D: L.6, S.7, G.8, G.9, K.23, Q.80, P.83, D.84, G.85, L.86, L.106, D.108, N.109, F.143, G.144, E.159, K.160, V.170, G.172, Y.174, R.192, W.221 Ligands: SO4.20 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:L.86 Hydrogen bonds: D:G.8, D:G.8, D:K.23, D:K.23, D:Q.80, D:Q.80, D:G.85, D:N.109, D:N.109, D:G.144, D:E.159, D:V.170 Water bridges: D:R.13, D:G.107, D:D.108 Salt bridges: D:K.160, D:K.160, D:R.192

4 x THM: THYMIDINE(Non-covalent)

THM.2: 13 residues within 4Å: Chain A: L.43, Y.112, G.113, F.116, T.117, V.248, A.249, E.253, I.254, R.257 Chain B: R.217, G.218 Ligands: SO4.5 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.43 Hydrogen bonds: A:G.113, A:G.113, A:K.247, A:A.249 Water bridges: A:C.250 pi-Cation interactions: B:R.217 THM.7: 13 residues within 4Å: Chain A: R.217, G.218 Chain B: L.43, Y.112, G.113, F.116, T.117, V.248, A.249, E.253, I.254, R.257 Ligands: SO4.10 8 PLIP interactions: 1 interactions with chain A, 7 interactions with chain B pi-Cation interactions: A:R.217 Hydrophobic interactions: B:L.43 Hydrogen bonds: B:Y.112, B:G.113, B:G.113, B:A.249 Water bridges: B:C.250, B:E.253 THM.13: 13 residues within 4Å: Chain C: L.43, Y.112, G.113, F.116, T.117, V.248, A.249, E.253, I.254, R.257 Chain D: R.217, G.218 Ligands: SO4.16 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.43 Hydrogen bonds: C:G.113, C:G.113, C:K.247, C:A.249 Water bridges: C:G.115, C:C.250 pi-Cation interactions: D:R.217 THM.19: 13 residues within 4Å: Chain C: R.217, G.218 Chain D: L.43, Y.112, G.113, F.116, T.117, V.248, A.249, E.253, I.254, R.257 Ligands: SO4.22 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.43 Hydrogen bonds: D:Y.112, D:G.113, D:G.113, D:K.247, D:A.249 Water bridges: D:C.250 pi-Cation interactions: C:R.217

14 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 5 residues within 4Å: Chain A: S.10, G.11, T.12, R.13 Ligands: UPG.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.10, A:G.11, A:T.12, A:R.13 Salt bridges: A:K.23 SO4.4: 4 residues within 4Å: Chain A: G.67, G.68, S.69, E.70 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.67, A:G.68, A:S.69, A:S.69, A:E.70 SO4.5: 6 residues within 4Å: Chain A: H.114, G.115 Chain B: G.216, R.217, G.218 Ligands: THM.2 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.115, A:E.118, B:R.217, B:G.218 Water bridges: A:H.114, B:G.216 Salt bridges: A:H.114 SO4.8: 5 residues within 4Å: Chain B: S.10, G.11, T.12, R.13 Ligands: UPG.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.10, B:G.11, B:T.12, B:R.13 Salt bridges: B:R.13, B:K.23 SO4.9: 5 residues within 4Å: Chain B: G.66, G.67, G.68, S.69, E.70 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.67, B:G.68, B:S.69 SO4.10: 6 residues within 4Å: Chain A: G.216, R.217, G.218 Chain B: H.114, G.115 Ligands: THM.7 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.217, A:G.218, B:G.115 Salt bridges: B:H.114 SO4.11: 4 residues within 4Å: Chain A: R.142, Q.232 Chain B: K.242, R.243 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.232 Salt bridges: A:R.142, B:R.243 Water bridges: B:R.243 SO4.14: 5 residues within 4Å: Chain C: S.10, G.11, T.12, R.13 Ligands: UPG.12 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.10, C:G.11, C:T.12 SO4.15: 5 residues within 4Å: Chain C: G.66, G.67, G.68, S.69, E.70 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.67, C:G.68, C:S.69, C:S.69 SO4.16: 6 residues within 4Å: Chain C: H.114, G.115 Chain D: G.216, R.217, G.218 Ligands: THM.13 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.115, D:G.218 Water bridges: C:G.113 Salt bridges: C:H.114 SO4.17: 5 residues within 4Å: Chain C: K.242, R.243 Chain D: R.142, S.229, Q.232 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Salt bridges: C:R.243, D:R.142 Hydrogen bonds: D:Q.232 SO4.20: 5 residues within 4Å: Chain D: S.10, G.11, T.12, R.13 Ligands: UPG.18 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:S.10, D:G.11, D:T.12, D:T.12, D:R.13 Water bridges: D:R.13 Salt bridges: D:R.13, D:K.23 SO4.21: 4 residues within 4Å: Chain D: G.67, G.68, S.69, E.70 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.67, D:G.68, D:S.69, D:S.69, D:E.70, D:E.70 SO4.22: 6 residues within 4Å: Chain C: G.216, R.217, G.218 Chain D: H.114, G.115 Ligands: THM.19 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.115, C:R.217, C:G.218 Water bridges: D:T.117 Salt bridges: D:H.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, T.J. et al., Crystal structure of glucose 1-phosphate thymidylyltransferase from Aneurinibacillus thermoaerophilus complexed with UDP-glucose and thymidine. TO BE PUBLISHED

Release Date

2013-10-23

Peptides

Glucose-1-phosphate thymidylyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glucose-1-phosphate thymidylyltransferase

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