SMTL ID : 3s4y.1

Crystal structure of human thiamin pyrophosphokinase 1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 18 residues within 4Å: Chain A: D.75, D.77, S.78, Q.100, D.101, H.102, T.103, D.104, R.135, Q.138 Chain B: W.206, L.208, S.220, T.221, S.222, N.223 Ligands: SO4.2, CA.3 15 PLIP interactions: 9 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:S.78, A:S.78, A:Q.100, A:D.104, A:Q.138, B:S.222 Water bridges: A:Q.100, A:Q.100, A:F.105, B:T.221, B:T.221 Salt bridges: A:R.135 Hydrophobic interactions: B:W.206, B:W.206, B:L.208 TPP.10: 17 residues within 4Å: Chain A: W.206, L.208, S.220, T.221, S.222, N.223 Chain B: D.75, D.77, Q.100, D.101, H.102, T.103, D.104, R.135, Q.138 Ligands: SO4.11, CA.12 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:Q.100, B:D.101, B:D.104, B:Q.138, A:T.221, A:S.222 Water bridges: B:Q.100, B:Q.100, B:F.105, B:R.135 Salt bridges: B:R.135 Hydrophobic interactions: A:W.206, A:W.206, A:L.208 TPP.19: 18 residues within 4Å: Chain C: D.75, D.77, S.78, Q.100, D.101, H.102, T.103, D.104, R.135, Q.138 Chain D: W.206, L.208, S.220, T.221, S.222, N.223 Ligands: SO4.20, CA.21 16 PLIP interactions: 6 interactions with chain D, 10 interactions with chain C Hydrophobic interactions: D:W.206, D:W.206, D:L.208 Hydrogen bonds: D:S.222, C:S.78, C:S.78, C:Q.100, C:D.101, C:D.104, C:Q.138 Water bridges: D:T.221, D:T.221, C:Q.100, C:Q.100, C:F.105 Salt bridges: C:R.135 TPP.28: 17 residues within 4Å: Chain C: W.206, L.208, S.220, T.221, S.222, N.223 Chain D: D.75, D.77, Q.100, D.101, H.102, T.103, D.104, R.135, Q.138 Ligands: SO4.29, CA.30 14 PLIP interactions: 5 interactions with chain C, 9 interactions with chain D Hydrophobic interactions: C:W.206, C:W.206, C:L.208 Hydrogen bonds: C:T.221, C:S.222, D:Q.100, D:D.104, D:D.104, D:Q.138 Water bridges: D:Q.100, D:Q.100, D:F.105, D:R.135 Salt bridges: D:R.135

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

SO4.2: 10 residues within 4Å: Chain A: N.29, A.49, D.50, G.51, D.77, S.78, D.104, Q.138 Ligands: TPP.1, CA.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.29, A:A.49, A:G.51, A:S.78, A:D.104, A:Q.138 Water bridges: A:N.29, A:D.104 SO4.4: 4 residues within 4Å: Chain A: E.61, G.62, E.63, R.64 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.62, A:R.64 Water bridges: A:E.61, A:R.64, A:E.65 Salt bridges: A:R.64 SO4.11: 10 residues within 4Å: Chain B: N.29, A.49, D.50, G.51, D.77, S.78, D.104, Q.138 Ligands: TPP.10, CA.12 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.29, B:G.51, B:S.78 Water bridges: B:N.29, B:A.49, B:D.104 SO4.13: 4 residues within 4Å: Chain B: E.61, G.62, E.63, R.64 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.62, B:R.64 Water bridges: B:R.64, B:R.64, B:E.65 Salt bridges: B:R.64 SO4.14: 3 residues within 4Å: Chain B: R.37, H.38, N.41 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.37, B:N.41 Salt bridges: B:H.38 SO4.20: 10 residues within 4Å: Chain C: N.29, A.49, D.50, G.51, D.77, S.78, D.104, Q.138 Ligands: TPP.19, CA.21 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.29, C:A.49, C:G.51, C:S.78, C:Q.138 Water bridges: C:N.29, C:D.104 SO4.22: 4 residues within 4Å: Chain C: E.61, G.62, E.63, R.64 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.62, C:R.64 Water bridges: C:R.64, C:R.64, C:E.65, C:Y.86, C:Y.86 Salt bridges: C:R.64 SO4.29: 10 residues within 4Å: Chain D: N.29, A.49, D.50, G.51, D.77, S.78, D.104, Q.138 Ligands: TPP.28, CA.30 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.29, D:D.50, D:G.51, D:S.78 Water bridges: D:N.29, D:A.49, D:D.104 SO4.31: 4 residues within 4Å: Chain D: E.61, G.62, E.63, R.64 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:G.62, D:R.64 Water bridges: D:R.64, D:R.64, D:E.65, D:Y.86, D:Y.86 Salt bridges: D:R.64 SO4.32: 3 residues within 4Å: Chain D: R.37, H.38, N.41 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.37, D:N.41 Salt bridges: D:H.38

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: D.50, D.75, D.77, D.104 Ligands: TPP.1, SO4.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.50, A:D.75, A:D.77, A:D.104 CA.12: 6 residues within 4Å: Chain B: D.50, D.75, D.77, D.104 Ligands: TPP.10, SO4.11 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.50, B:D.75, B:D.77, B:D.104 CA.21: 6 residues within 4Å: Chain C: D.50, D.75, D.77, D.104 Ligands: TPP.19, SO4.20 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.50, C:D.75, C:D.77, C:D.104 CA.30: 6 residues within 4Å: Chain D: D.50, D.75, D.77, D.104 Ligands: TPP.28, SO4.29 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.50, D:D.75, D:D.77, D:D.104

18 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.5: 2 residues within 4Å: Chain A: D.33, N.34 Ligand excluded by PLIP UNX.6: 4 residues within 4Å: Chain A: A.133 Chain B: A.133, G.134 Ligands: UNX.9 Ligand excluded by PLIP UNX.7: 4 residues within 4Å: Chain A: H.102, T.103, T.106, Q.148 Ligand excluded by PLIP UNX.8: 1 residues within 4Å: Chain A: R.55 Ligand excluded by PLIP UNX.9: 4 residues within 4Å: Chain A: A.133, G.134 Chain B: A.133 Ligands: UNX.6 Ligand excluded by PLIP UNX.15: 1 residues within 4Å: Chain B: R.55 Ligand excluded by PLIP UNX.16: 2 residues within 4Å: Chain B: H.102, T.106 Ligand excluded by PLIP UNX.17: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.18: 1 residues within 4Å: Chain B: R.46 Ligand excluded by PLIP UNX.23: 2 residues within 4Å: Chain C: D.33, N.34 Ligand excluded by PLIP UNX.24: 4 residues within 4Å: Chain C: A.133 Chain D: A.133, G.134 Ligands: UNX.27 Ligand excluded by PLIP UNX.25: 4 residues within 4Å: Chain C: H.102, T.103, T.106, Q.148 Ligand excluded by PLIP UNX.26: 1 residues within 4Å: Chain C: R.55 Ligand excluded by PLIP UNX.27: 4 residues within 4Å: Chain C: A.133, G.134 Chain D: A.133 Ligands: UNX.24 Ligand excluded by PLIP UNX.33: 1 residues within 4Å: Chain D: R.55 Ligand excluded by PLIP UNX.34: 2 residues within 4Å: Chain D: H.102, T.106 Ligand excluded by PLIP UNX.35: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.36: 1 residues within 4Å: Chain D: R.46 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, L. et al., Crystal structure of human thiamin pyrophosphokinase 1. to be published

Release Date

2011-06-08

Peptides

Thiamin pyrophosphokinase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Thiamin pyrophosphokinase 1