SMTL ID : 1h5r.1

Thymidylyltransferase complexed with Thimidine and Glucose-1-phospate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-3-1-mer

Ligands

8 x THM: THYMIDINE(Non-covalent)

THM.1: 13 residues within 4Å: Chain A: L.46, Y.115, G.116, L.119, K.250, V.251, S.252, E.256, I.257, R.260 Chain D: R.220, G.221 Ligands: SO4.4 10 PLIP interactions: 4 interactions with chain D, 6 interactions with chain A Hydrogen bonds: D:G.221, A:G.116, A:G.116, A:S.252 Water bridges: D:R.220, D:R.220, A:C.253, A:E.256 pi-Cation interactions: D:R.220 Hydrophobic interactions: A:L.46 THM.2: 12 residues within 4Å: Chain A: L.9, G.11, G.12, Q.27, Q.83, P.86, D.87, G.88, L.89, D.111, E.197 Ligands: G1P.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.89 Hydrogen bonds: A:G.11, A:Q.83, A:Q.83, A:G.88, A:D.111 Water bridges: A:G.12, A:G.12, A:G.110 THM.6: 11 residues within 4Å: Chain B: L.46, F.114, Y.115, G.116, D.118, L.119, P.120, V.251, S.252, I.257 Ligands: SO4.9 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.46 Hydrogen bonds: B:G.116, B:L.119, B:S.252 Water bridges: B:C.253, B:E.256 THM.7: 13 residues within 4Å: Chain B: L.9, G.11, G.12, Q.27, Q.83, P.86, D.87, G.88, L.89, L.109, D.111, E.197 Ligands: G1P.8 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.89 Hydrogen bonds: B:G.11, B:Q.83, B:Q.83, B:G.88, B:D.111 Water bridges: B:G.12, B:G.12, B:G.110, B:D.111 THM.10: 12 residues within 4Å: Chain B: G.221 Chain C: L.46, Y.115, G.116, H.117, D.118, L.119, P.120, V.251, S.252, I.257 Ligands: SO4.13 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.46, C:L.46 Hydrogen bonds: C:G.116, C:G.116, C:D.118, C:L.119, C:S.252 Water bridges: C:C.253, C:E.256 pi-Cation interactions: B:R.220 THM.11: 14 residues within 4Å: Chain C: L.9, A.10, G.11, G.12, Q.27, Q.83, P.86, D.87, G.88, L.89, L.109, D.111, E.197 Ligands: G1P.12 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.89 Hydrogen bonds: C:G.11, C:G.12, C:Q.83, C:Q.83, C:G.88, C:D.111, C:D.111 THM.14: 15 residues within 4Å: Chain A: R.220 Chain D: L.46, Y.115, G.116, H.117, D.118, L.119, P.120, K.250, V.251, S.252, E.256, I.257, R.260 Ligands: SO4.17 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:L.46 Hydrogen bonds: D:G.116, D:G.116, D:D.118, D:L.119, D:S.252 Water bridges: D:D.118, D:D.118, D:C.253 pi-Cation interactions: A:R.220 THM.15: 13 residues within 4Å: Chain D: L.9, G.11, G.12, Q.27, Q.83, P.86, D.87, G.88, L.89, G.110, D.111, E.197 Ligands: G1P.16 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:L.89 Hydrogen bonds: D:G.11, D:Q.83, D:Q.83, D:G.88, D:G.110, D:D.111, D:D.111 Water bridges: D:G.12, D:G.12

4 x G1P: 1-O-phosphono-alpha-D-glucopyranose(Non-covalent)

G1P.3: 15 residues within 4Å: Chain A: L.89, L.109, Y.146, G.147, E.162, K.163, V.173, T.174, G.175, Y.177, E.197, I.200, T.201, W.224 Ligands: THM.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.147, A:G.147, A:E.162, A:E.162, A:T.201 Water bridges: A:L.89, A:Y.177, A:Y.177, A:E.197, A:T.201 Salt bridges: A:K.163 G1P.8: 13 residues within 4Å: Chain B: L.89, L.109, Y.146, G.147, E.162, K.163, V.173, T.174, G.175, R.195, T.201, W.224 Ligands: THM.7 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.147, B:E.162, B:E.162, B:Y.177 Salt bridges: B:R.195 G1P.12: 13 residues within 4Å: Chain C: L.89, L.109, Y.146, G.147, E.162, K.163, V.173, G.175, Y.177, R.195, T.201, W.224 Ligands: THM.11 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:G.147, C:E.162, C:R.195, C:T.201 Water bridges: C:D.111, C:V.173, C:T.174, C:G.175, C:E.199, C:T.201 Salt bridges: C:K.163, C:R.195 G1P.16: 12 residues within 4Å: Chain D: L.89, L.109, N.112, Y.146, G.147, E.162, K.163, V.173, G.175, T.201, W.224 Ligands: THM.15 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:N.112, D:N.112, D:G.147, D:G.147, D:E.162, D:R.195 Water bridges: D:R.16, D:Y.177, D:Y.177, D:I.200, D:T.201 Salt bridges: D:K.163

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

SO4.4: 6 residues within 4Å: Chain A: H.117, D.118 Chain D: G.219, R.220, G.221 Ligands: THM.1 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:R.220, D:G.221, A:D.118 Water bridges: D:G.219 Salt bridges: A:H.117 SO4.5: 2 residues within 4Å: Chain A: R.4, V.127 5 PLIP interactions: 5 interactions with chain A Water bridges: A:D.104, A:V.127, A:V.127, A:E.130 Salt bridges: A:R.4 SO4.9: 6 residues within 4Å: Chain B: H.117, D.118 Chain C: G.219, R.220, G.221 Ligands: THM.6 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:D.118, C:R.220, C:G.221 Salt bridges: B:H.117 SO4.13: 6 residues within 4Å: Chain B: G.219, R.220, G.221 Chain C: H.117, D.118 Ligands: THM.10 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:G.221, C:D.118 Water bridges: B:R.220, B:R.220 Salt bridges: C:H.117 SO4.17: 6 residues within 4Å: Chain A: G.219, R.220, G.221 Chain D: H.117, D.118 Ligands: THM.14 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:D.118, D:D.118, A:R.220, A:G.221 Salt bridges: D:H.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zuccotti, S. et al., Kinetic and Crystallographic Analyses Support a Sequential-Ordered Bi Bi Catalytic Mechanism for Escherichia Coli Glucose-1-Phosphate Thymidylyltransferase. J.Mol.Biol. (2001)

Release Date

2001-11-23

Peptides

GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE: ACD
GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

D
D

B
B

GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE

GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE

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