- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.50 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 12 x SO4: SULFATE ION(Non-functional Binders)
SO4.2: 4 residues within 4Å:- Chain A: G.78, E.79, R.80
- Ligands: SO4.5
7 PLIP interactions:7 interactions with chain A- Hydrogen bonds: A:G.78, A:G.78, A:R.80
- Water bridges: A:E.81, A:E.81, A:Y.102
- Salt bridges: A:R.80
SO4.3: 8 residues within 4Å:- Chain A: D.117, H.118, T.119, T.122, N.160, T.161, Q.164
- Ligands: PYI.7
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:D.117, A:T.119, A:N.160, A:Q.164
- Salt bridges: A:H.118
SO4.4: 1 residues within 4Å:- Chain A: R.62
1 PLIP interactions:1 interactions with chain A- Salt bridges: A:R.62
SO4.5: 4 residues within 4Å:- Chain A: Y.102, K.105, K.106
- Ligands: SO4.2
2 PLIP interactions:2 interactions with chain A- Salt bridges: A:K.105, A:K.106
SO4.6: 6 residues within 4Å:- Chain A: L.162, V.171, P.172, I.173, Y.183, Q.186
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:I.173, A:I.173, A:Q.186
SO4.10: 5 residues within 4Å:- Chain B: E.77, G.78, E.79, R.80, Y.102
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:G.78, B:R.80, B:Y.102
- Water bridges: B:E.81
- Salt bridges: B:R.80
SO4.14: 4 residues within 4Å:- Chain C: G.78, E.79, R.80
- Ligands: SO4.17
8 PLIP interactions:8 interactions with chain C- Hydrogen bonds: C:G.78, C:G.78, C:R.80
- Water bridges: C:E.81, C:E.81, C:E.81, C:E.81
- Salt bridges: C:R.80
SO4.15: 8 residues within 4Å:- Chain C: D.117, H.118, T.119, T.122, N.160, T.161, Q.164
- Ligands: PYI.19
7 PLIP interactions:7 interactions with chain C- Hydrogen bonds: C:D.117, C:T.119, C:T.122, C:N.160, C:T.161, C:Q.164
- Salt bridges: C:H.118
SO4.16: 1 residues within 4Å:- Chain C: R.62
1 PLIP interactions:1 interactions with chain C- Salt bridges: C:R.62
SO4.17: 4 residues within 4Å:- Chain C: Y.102, K.105, K.106
- Ligands: SO4.14
3 PLIP interactions:3 interactions with chain C- Water bridges: C:E.81
- Salt bridges: C:K.105, C:K.106
SO4.18: 6 residues within 4Å:- Chain C: L.162, V.171, P.172, I.173, Y.183, Q.186
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:I.173, C:I.173, C:Q.186
SO4.22: 5 residues within 4Å:- Chain D: E.77, G.78, E.79, R.80, Y.102
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:G.78, D:R.80
- Water bridges: D:E.81
- Salt bridges: D:R.80
- 4 x PYI: 1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-2-METHYLPYRIDINIUM(Non-covalent)
PYI.7: 16 residues within 4Å:- Chain A: D.91, D.93, Q.116, D.117, H.118, T.119, D.120, R.151, Q.154
- Chain B: W.222, S.236, T.237, S.238
- Ligands: MG.1, SO4.3, AMP.8
14 PLIP interactions:6 interactions with chain A, 8 interactions with chain B- Hydrophobic interactions: A:T.119, B:W.222, B:W.222, B:W.222
- Hydrogen bonds: A:D.117, A:D.120, A:Q.154, B:S.238, B:S.238
- Water bridges: A:K.123, B:T.237, B:T.237
- Salt bridges: A:R.151
- pi-Stacking: B:W.222
PYI.12: 16 residues within 4Å:- Chain A: W.222, L.224, S.236, T.237, S.238, N.239
- Chain B: D.91, S.94, Q.116, D.117, H.118, T.119, D.120, R.151
- Ligands: MG.9, EPE.11
13 PLIP interactions:9 interactions with chain B, 4 interactions with chain A- Hydrophobic interactions: B:T.119, A:W.222, A:W.222, A:L.224
- Hydrogen bonds: B:D.91, B:S.94, B:S.94, B:Q.116, B:D.120, A:S.238
- Water bridges: B:R.151, B:R.151
- Salt bridges: B:R.151
PYI.19: 16 residues within 4Å:- Chain C: D.91, D.93, Q.116, D.117, H.118, T.119, D.120, R.151, Q.154
- Chain D: W.222, S.236, T.237, S.238
- Ligands: MG.13, SO4.15, AMP.20
15 PLIP interactions:8 interactions with chain D, 7 interactions with chain C- Hydrophobic interactions: D:W.222, D:W.222, D:W.222, C:T.119
- Hydrogen bonds: D:S.238, D:S.238, C:D.117, C:D.117, C:D.120, C:Q.154
- Water bridges: D:T.237, D:T.237, C:K.123
- pi-Stacking: D:W.222
- Salt bridges: C:R.151
PYI.24: 16 residues within 4Å:- Chain C: W.222, L.224, S.236, T.237, S.238, N.239
- Chain D: D.91, S.94, Q.116, D.117, H.118, T.119, D.120, R.151
- Ligands: MG.21, EPE.23
14 PLIP interactions:4 interactions with chain C, 10 interactions with chain D- Hydrophobic interactions: C:W.222, C:W.222, C:L.224, D:T.119
- Hydrogen bonds: C:S.238, D:D.91, D:S.94, D:S.94, D:Q.116, D:D.117, D:D.120
- Water bridges: D:R.151, D:R.151
- Salt bridges: D:R.151
- 2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)
AMP.8: 19 residues within 4Å:- Chain A: L.44, N.45, Q.46, A.65, D.66, G.67, D.93, S.94, T.119, D.120, F.121, G.147, G.149, G.150, R.151, Q.154, S.158
- Ligands: MG.1, PYI.7
12 PLIP interactions:12 interactions with chain A- Hydrogen bonds: A:N.45, A:N.45, A:D.66, A:G.67, A:S.94, A:S.94, A:D.120, A:F.121, A:G.149, A:R.151, A:Q.154
- Water bridges: A:R.151
AMP.20: 19 residues within 4Å:- Chain C: L.44, N.45, Q.46, A.65, D.66, G.67, D.93, S.94, T.119, D.120, F.121, G.147, G.149, G.150, R.151, Q.154, S.158
- Ligands: MG.13, PYI.19
12 PLIP interactions:12 interactions with chain C- Hydrogen bonds: C:N.45, C:N.45, C:G.67, C:D.93, C:S.94, C:D.120, C:D.120, C:F.121, C:G.149, C:R.151, C:Q.154
- Water bridges: C:R.151
- 2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)
EPE.11: 15 residues within 4Å:- Chain B: L.44, N.45, A.65, D.66, G.67, S.94, T.119, D.120, F.121, Q.154, A.157, S.158, T.161
- Ligands: MG.9, PYI.12
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:G.67, B:S.94, B:T.161, B:T.161
EPE.23: 15 residues within 4Å:- Chain D: L.44, N.45, A.65, D.66, G.67, S.94, T.119, D.120, F.121, Q.154, A.157, S.158, T.161
- Ligands: MG.21, PYI.24
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:G.67, D:S.94, D:T.119, D:T.161, D:T.161
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Liu, J.Y. et al., Pyrithiamine as a substrate for thiamine pyrophosphokinase. J.Biol.Chem. (2006)
- Release Date
- 2005-11-29
- Peptides
- Thiamin pyrophosphokinase 1: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.50 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 12 x SO4: SULFATE ION(Non-functional Binders)
- 4 x PYI: 1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-2-METHYLPYRIDINIUM(Non-covalent)
- 2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)
- 2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Liu, J.Y. et al., Pyrithiamine as a substrate for thiamine pyrophosphokinase. J.Biol.Chem. (2006)
- Release Date
- 2005-11-29
- Peptides
- Thiamin pyrophosphokinase 1: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B