- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.70 Å
- Oligo State
- homo-tetramer
- Ligands
- 5 x CL: CHLORIDE ION(Non-functional Binders)
- 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
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- 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
AB
BC
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.70 Å
- Oligo State
- homo-tetramer
- Ligands
- 5 x CL: CHLORIDE ION(Non-functional Binders)
- 2 x SO4: SULFATE ION(Non-functional Binders)
- 8 x TYD: THYMIDINE-5'-DIPHOSPHATE(Non-covalent)
- 11 x GOL: GLYCEROL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- 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
AB
BC
CD
D