SMTL ID : 1lvw.1

Crystal structure of glucose-1-phosphate thymidylyltransferase, RmlA, complex with dTDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 3 residues within 4Å: Chain A: V.173, T.201, N.204 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain B: T.201, N.204 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain C: T.201, N.204 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: K.168 Chain C: H.294 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain D: T.201, N.204 Ligand excluded by PLIP

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

SO4.2: 3 residues within 4Å: Chain A: S.202, E.205, R.209 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.202 Water bridges: A:S.202, A:S.202, A:R.209, A:R.209 Salt bridges: A:R.209 SO4.22: 2 residues within 4Å: Chain D: Y.259, R.266 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.259, D:Y.259 Water bridges: D:R.266 Salt bridges: D:R.266

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

TYD.3: 16 residues within 4Å: Chain A: L.9, A.10, G.11, G.12, K.26, Q.27, Q.83, P.86, R.87, G.88, I.89, L.109, G.110, D.111, E.197 Ligands: GOL.6 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.11, A:Q.83, A:Q.83, A:G.88, A:G.110, A:D.111, A:D.111, A:D.111 Water bridges: A:G.12, A:N.112, A:R.195 Salt bridges: A:K.26 TYD.4: 13 residues within 4Å: Chain A: L.46, Y.115, G.116, H.117, R.118, F.119, S.120, Y.250, I.251, A.252, E.256, I.257 Chain C: R.220 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:L.46 Hydrogen bonds: A:G.116, A:R.118, A:F.119, A:S.120, A:S.120, A:Y.250, A:A.252 Water bridges: A:S.42, A:Y.115, A:R.118, A:S.120, A:S.120, A:E.121, A:C.253, C:R.220 Salt bridges: A:H.117 pi-Cation interactions: C:R.220 TYD.9: 15 residues within 4Å: Chain B: L.9, A.10, G.11, G.12, K.26, Q.27, Q.83, P.86, R.87, G.88, I.89, L.109, G.110, D.111, E.197 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:P.86, B:I.89 Hydrogen bonds: B:G.11, B:Q.83, B:Q.83, B:G.88, B:G.110, B:D.111, B:D.111, B:D.111 Water bridges: B:G.12, B:K.26, B:K.26, B:N.112 Salt bridges: B:K.26 TYD.10: 13 residues within 4Å: Chain B: L.46, Y.115, G.116, H.117, R.118, F.119, S.120, Y.250, I.251, A.252, E.256, I.257 Chain D: R.220 18 PLIP interactions: 14 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:L.46, B:L.46 Hydrogen bonds: B:G.116, B:G.116, B:R.118, B:F.119, B:S.120, B:Y.250, B:A.252, D:R.220 Water bridges: B:S.120, B:S.120, B:E.121, B:R.124, D:R.220, D:R.220 Salt bridges: B:H.117 pi-Cation interactions: D:R.220 TYD.16: 15 residues within 4Å: Chain C: L.9, A.10, G.11, G.12, K.26, Q.27, Q.83, P.86, R.87, G.88, I.89, L.109, G.110, D.111 Ligands: GOL.19 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:G.11, C:Q.83, C:Q.83, C:G.88, C:G.110, C:D.111, C:D.111, C:D.111 Water bridges: C:G.12, C:G.12, C:N.112 Salt bridges: C:K.26 TYD.17: 13 residues within 4Å: Chain A: R.220 Chain C: L.46, Y.115, G.116, H.117, R.118, F.119, S.120, Y.250, I.251, A.252, E.256, I.257 19 PLIP interactions: 15 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:L.46 Hydrogen bonds: C:G.116, C:G.116, C:R.118, C:F.119, C:S.120, C:S.120, C:Y.250, C:A.252 Water bridges: C:S.42, C:R.118, C:S.120, C:S.120, C:E.121, A:R.220, A:R.220, A:R.220 Salt bridges: C:H.117 pi-Cation interactions: A:R.220 TYD.23: 15 residues within 4Å: Chain D: L.9, A.10, G.11, G.12, K.26, Q.27, Q.83, P.86, R.87, G.88, I.89, L.109, G.110, D.111 Ligands: GOL.25 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:G.11, D:Q.83, D:Q.83, D:G.88, D:G.110, D:D.111, D:D.111, D:D.111 Water bridges: D:G.12, D:G.12, D:N.112 Salt bridges: D:K.26 TYD.24: 12 residues within 4Å: Chain B: R.220 Chain D: L.46, Y.115, G.116, H.117, R.118, F.119, S.120, I.251, A.252, E.256, I.257 16 PLIP interactions: 12 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: D:L.46, D:L.46 Hydrogen bonds: D:G.116, D:R.118, D:F.119, D:S.120, D:A.252, B:R.220 Water bridges: D:S.42, D:E.121, D:E.121, D:Y.250, B:R.220, B:R.220 Salt bridges: D:H.117 pi-Cation interactions: B:R.220

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: V.140, R.141, D.142, F.146 Chain C: K.245, R.246, Q.247, G.248 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:Q.247, A:R.141, A:D.142 GOL.6: 9 residues within 4Å: Chain A: K.26, D.111, W.224, L.225, D.226, T.227, G.228 Chain C: R.246 Ligands: TYD.3 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:K.26, A:L.225, A:T.227, A:T.227, A:G.228, C:R.246 Water bridges: A:N.112 GOL.7: 5 residues within 4Å: Chain A: E.150, F.151, K.168, S.169 Chain C: H.294 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:H.294, A:F.151 GOL.11: 8 residues within 4Å: Chain B: V.140, R.141, D.142, F.146 Chain D: K.245, R.246, Q.247, G.248 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:Q.247, B:R.141, B:D.142 GOL.12: 7 residues within 4Å: Chain B: R.125, V.134, E.154, G.155, R.214, V.215, E.216 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.154, B:E.216 Water bridges: B:R.125, B:R.214 GOL.13: 7 residues within 4Å: Chain B: R.246 Chain D: Y.138, F.146, W.224, L.225, D.226 Ligands: GOL.25 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.246, B:R.246 GOL.18: 9 residues within 4Å: Chain A: K.245, R.246, Q.247, G.248 Chain C: V.140, R.141, D.142, F.146 Ligands: GOL.20 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:R.246, A:Q.247, C:R.141, C:D.142 Water bridges: A:R.246 GOL.19: 8 residues within 4Å: Chain C: K.26, D.111, L.225, D.226, T.227, G.228 Ligands: TYD.16, GOL.20 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:K.26, C:D.111, C:L.225, C:D.226, C:T.227, C:T.227, C:G.228 GOL.20: 7 residues within 4Å: Chain A: R.246 Chain C: F.146, W.224, L.225, D.226 Ligands: GOL.18, GOL.19 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:D.226, A:R.246, A:R.246 Water bridges: A:R.246, A:R.246 GOL.25: 8 residues within 4Å: Chain D: K.26, D.111, L.225, D.226, T.227, G.228 Ligands: GOL.13, TYD.23 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:K.26, D:L.225, D:T.227, D:T.227, D:T.227, D:G.228 GOL.26: 8 residues within 4Å: Chain B: K.245, R.246, Q.247, G.248 Chain D: R.141, D.142, P.145, F.146 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:R.141, D:D.142, D:D.142, B:K.245 Water bridges: D:R.141, B:R.246

Links

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Citation

Dong, A. et al., Crystal structure of glucose-1-phosphate thymidylyltransferase, RmlA, complex with dTDP. To be Published

Release Date

2003-07-29

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