SMTL ID : 1h5t.1

Thymidylyltransferase complexed with Thymidylyldiphosphate-glucose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-3-1-mer

Ligands

4 x TYD: THYMIDINE-5'-DIPHOSPHATE(Non-covalent)

TYD.1: 15 residues within 4Å: Chain A: L.46, Y.115, G.116, H.117, D.118, L.119, P.120, K.250, V.251, S.252, E.256, I.257 Chain D: G.219, R.220, G.221 13 PLIP interactions: 4 interactions with chain D, 9 interactions with chain A Hydrogen bonds: D:R.220, D:G.221, A:G.116, A:G.116, A:D.118, A:D.118, A:L.119, A:S.252 Water bridges: D:R.220, A:K.250 pi-Cation interactions: D:R.220 Hydrophobic interactions: A:L.46 Salt bridges: A:H.117 TYD.3: 14 residues within 4Å: Chain B: L.46, Y.115, G.116, H.117, D.118, L.119, V.251, S.252, E.256, I.257, R.260 Chain C: G.219, R.220, G.221 12 PLIP interactions: 7 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:L.46 Hydrogen bonds: B:G.116, B:D.118, B:S.252, C:R.220, C:G.221 Water bridges: B:C.253, B:C.253, C:R.220, C:R.220 Salt bridges: B:H.117 pi-Cation interactions: C:R.220 TYD.5: 14 residues within 4Å: Chain B: G.219, R.220, G.221 Chain C: L.46, Y.115, G.116, H.117, D.118, K.250, V.251, S.252, E.256, I.257, R.260 13 PLIP interactions: 9 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:L.46 Hydrogen bonds: C:G.116, C:G.116, C:D.118, C:S.252, B:R.220, B:G.221 Water bridges: C:H.117, C:C.253, B:G.219 Salt bridges: C:H.117, C:H.117 pi-Cation interactions: B:R.220 TYD.7: 13 residues within 4Å: Chain A: G.219, R.220, G.221 Chain D: L.46, Y.115, G.116, H.117, D.118, P.120, V.251, S.252, E.256, I.257 13 PLIP interactions: 10 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:L.46 Hydrogen bonds: D:G.116, D:G.116, D:D.118, D:S.252, A:R.220 Water bridges: D:H.117, D:H.117, D:K.250, D:E.256, A:R.220 Salt bridges: D:H.117 pi-Cation interactions: A:R.220

4 x DAU: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE(Non-covalent)

DAU.2: 22 residues within 4Å: Chain A: L.9, A.10, G.11, G.12, Q.27, Q.83, P.86, D.87, G.88, L.89, L.109, D.111, Y.146, G.147, E.162, K.163, V.173, Y.177, R.195, E.197, T.201, W.224 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:G.11, A:K.26, A:Q.83, A:Q.83, A:G.88, A:D.111, A:G.147, A:E.162, A:V.173, A:R.195, A:T.201 Water bridges: A:G.12, A:G.12, A:L.89, A:D.111, A:D.111, A:Y.177, A:Y.177, A:R.195, A:R.195, A:I.200 Salt bridges: A:K.163, A:K.163, A:R.195 DAU.4: 19 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, Y.146, G.147, E.162, K.163, V.173, R.195, E.197, T.201 21 PLIP interactions: 21 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, B:G.147, B:E.162, B:V.173, B:R.195, B:E.199 Water bridges: B:G.12, B:L.89, B:G.110, B:D.111, B:N.112, B:I.200 Salt bridges: B:K.163, B:K.163, B:K.163, B:R.195 DAU.6: 23 residues within 4Å: Chain C: L.9, A.10, G.11, G.12, R.16, Q.27, Q.83, P.86, D.87, G.88, L.89, L.109, D.111, Y.146, G.147, E.162, K.163, V.173, Y.177, R.195, E.197, T.201, W.224 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:L.89 Hydrogen bonds: C:G.11, C:G.12, C:R.16, C:Q.83, C:Q.83, C:G.88, C:D.111, C:G.147, C:E.162, C:V.173, C:R.195, C:R.195, C:T.201 Water bridges: C:T.201 Salt bridges: C:K.163, C:K.163, C:K.163, C:R.195 DAU.8: 25 residues within 4Å: Chain D: L.9, A.10, G.11, G.12, Q.27, Q.83, P.86, D.87, G.88, L.89, L.109, G.110, D.111, N.112, Y.146, G.147, E.162, K.163, V.173, G.175, Y.177, R.195, E.197, T.201, W.224 21 PLIP interactions: 21 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, D:N.112, D:G.147, D:E.162, D:V.173, D:R.195 Water bridges: D:G.12, D:G.12, D:Y.177, D:Y.177, D:I.200 Salt bridges: D:K.163, D:K.163, D:K.163

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

SO4.9: 2 residues within 4Å: Chain D: K.81, V.82 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:V.82 Salt bridges: D:K.81

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 1: ACD
Glucose-1-phosphate thymidylyltransferase 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

D
D

B
B

Glucose-1-phosphate thymidylyltransferase 1

Glucose-1-phosphate thymidylyltransferase 1

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