SMTL ID : 2f17.2 (1 other biounit)

Mouse Thiamin Pyrophosphokinase in a Ternary Complex with Pyrithiamin Pyrophosphate and AMP at 2.5 angstrom

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.66, D.91, D.93, D.120 Ligands: PYI.7, AMP.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.66, A:D.91, A:D.93, A:D.120 MG.9: 5 residues within 4Å: Chain B: D.66, D.91, D.120 Ligands: EPE.11, PYI.12 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.66, B:D.91, B:D.120 MG.13: 6 residues within 4Å: Chain C: D.66, D.91, D.93, D.120 Ligands: PYI.19, AMP.20 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.66, C:D.91, C:D.93, C:D.120 MG.21: 5 residues within 4Å: Chain D: D.66, D.91, D.120 Ligands: EPE.23, PYI.24 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.66, D:D.91, D:D.120

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
A

B
B

C
A

D
B

Thiamin pyrophosphokinase 1

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