SMTL ID : 5lhu.1

ATP Phosphoribosyltransferase from Mycobacterium tuberculosis in complex with the allosteric inhibitor L-Histidine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-hexamer

Ligands

6 x HIS: HISTIDINE(Non-covalent)

HIS.1: 14 residues within 4Å: Chain A: Y.227, D.228, L.252, A.283, L.285 Chain C: G.243, L.244, E.245, S.246, P.247, T.248, R.261, A.262, L.263 12 PLIP interactions: 7 interactions with chain C, 3 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: C:L.244, C:E.245, C:S.246, C:S.246, C:T.248, C:L.263, A:D.228, A:A.283, H.1 Water bridges: C:T.248, A:Y.227 Salt bridges: H.1 HIS.9: 14 residues within 4Å: Chain A: G.243, L.244, E.245, S.246, P.247, T.248, R.261, A.262, L.263 Chain B: Y.227, D.228, L.252, A.283, L.285 12 PLIP interactions: 3 interactions with chain B, 7 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: B:D.228, B:A.283, A:L.244, A:E.245, A:S.246, A:S.246, A:T.248, A:L.263, H.9 Water bridges: B:Y.227, A:T.248 Salt bridges: H.9 HIS.17: 14 residues within 4Å: Chain B: G.243, L.244, E.245, S.246, P.247, T.248, R.261, A.262, L.263 Chain C: Y.227, D.228, L.252, A.283, L.285 12 PLIP interactions: 3 interactions with chain C, 7 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: C:D.228, C:A.283, B:L.244, B:E.245, B:S.246, B:S.246, B:T.248, B:L.263, H.17 Water bridges: C:Y.227, B:T.248 Salt bridges: H.17 HIS.25: 14 residues within 4Å: Chain D: Y.227, D.228, L.252, A.283, L.285 Chain F: G.243, L.244, E.245, S.246, P.247, T.248, R.261, A.262, L.263 12 PLIP interactions: 7 interactions with chain F, 3 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: F:L.244, F:E.245, F:S.246, F:S.246, F:T.248, F:T.248, F:L.263, D:D.228, D:A.283, H.25 Water bridges: D:Y.227 Salt bridges: H.25 HIS.33: 14 residues within 4Å: Chain D: G.243, L.244, E.245, S.246, P.247, T.248, R.261, A.262, L.263 Chain E: Y.227, D.228, L.252, A.283, L.285 12 PLIP interactions: 3 interactions with chain E, 7 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: E:D.228, E:A.283, D:L.244, D:E.245, D:S.246, D:S.246, D:T.248, D:T.248, D:L.263, H.33 Water bridges: E:Y.227 Salt bridges: H.33 HIS.41: 14 residues within 4Å: Chain E: G.243, L.244, E.245, S.246, P.247, T.248, R.261, A.262, L.263 Chain F: Y.227, D.228, L.252, A.283, L.285 12 PLIP interactions: 2 Ligand-Ligand interactions, 7 interactions with chain E, 3 interactions with chain F Hydrogen bonds: H.41, E:L.244, E:E.245, E:S.246, E:S.246, E:T.248, E:T.248, E:L.263, F:D.228, F:A.283 Salt bridges: H.41 Water bridges: F:Y.227

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

SO4.2: 4 residues within 4Å: Chain A: R.131, R.145 Chain D: R.145 Ligands: SO4.26 Ligand excluded by PLIP SO4.3: 6 residues within 4Å: Chain A: V.166, G.167, S.168, G.169, R.170, T.171 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain A: Q.155 Chain D: R.13, E.54, E.71 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain A: F.97, G.98, S.99 Chain C: R.36 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: G.109, R.110, N.111, W.112 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: R.90, R.92, D.207 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain B: R.131, R.145 Chain F: R.145 Ligands: SO4.42 Ligand excluded by PLIP SO4.11: 6 residues within 4Å: Chain B: V.166, G.167, S.168, G.169, R.170, T.171 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain B: Q.155 Chain F: R.13, E.54, E.71 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain A: R.36 Chain B: F.97, G.98, S.99 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain B: G.109, R.110, N.111, W.112 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain B: R.90, R.92, D.207 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain C: R.131, R.145 Chain E: R.145 Ligands: SO4.34 Ligand excluded by PLIP SO4.19: 6 residues within 4Å: Chain C: V.166, G.167, S.168, G.169, R.170, T.171 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain C: Q.155 Chain E: R.13, E.54, E.71 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain B: R.36 Chain C: F.97, G.98, S.99 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain C: G.109, R.110, N.111, W.112 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain C: R.90, R.92, D.207 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain A: R.145 Chain D: R.131, R.145 Ligands: SO4.2 Ligand excluded by PLIP SO4.27: 6 residues within 4Å: Chain D: V.166, G.167, S.168, G.169, R.170, T.171 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain A: R.13, E.54, E.71 Chain D: Q.155 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain D: F.97, G.98, S.99 Chain F: R.36 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain D: G.109, R.110, N.111, W.112 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain D: R.90, R.92, D.207 Ligand excluded by PLIP SO4.34: 4 residues within 4Å: Chain C: R.145 Chain E: R.131, R.145 Ligands: SO4.18 Ligand excluded by PLIP SO4.35: 6 residues within 4Å: Chain E: V.166, G.167, S.168, G.169, R.170, T.171 Ligand excluded by PLIP SO4.36: 4 residues within 4Å: Chain C: R.13, E.54, E.71 Chain E: Q.155 Ligand excluded by PLIP SO4.37: 4 residues within 4Å: Chain D: R.36 Chain E: F.97, G.98, S.99 Ligand excluded by PLIP SO4.38: 4 residues within 4Å: Chain E: G.109, R.110, N.111, W.112 Ligand excluded by PLIP SO4.39: 3 residues within 4Å: Chain E: R.90, R.92, D.207 Ligand excluded by PLIP SO4.42: 4 residues within 4Å: Chain B: R.145 Chain F: R.131, R.145 Ligands: SO4.10 Ligand excluded by PLIP SO4.43: 6 residues within 4Å: Chain F: V.166, G.167, S.168, G.169, R.170, T.171 Ligand excluded by PLIP SO4.44: 4 residues within 4Å: Chain B: R.13, E.54, E.71 Chain F: Q.155 Ligand excluded by PLIP SO4.45: 4 residues within 4Å: Chain E: R.36 Chain F: F.97, G.98, S.99 Ligand excluded by PLIP SO4.46: 4 residues within 4Å: Chain F: G.109, R.110, N.111, W.112 Ligand excluded by PLIP SO4.47: 3 residues within 4Å: Chain F: R.90, R.92, D.207 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 3 residues within 4Å: Chain A: T.113, T.114, G.181 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.114, A:T.114, A:G.181 Water bridges: A:A.115 GOL.16: 3 residues within 4Å: Chain B: T.113, T.114, G.181 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.114, B:T.114, B:G.181 Water bridges: B:A.115 GOL.24: 3 residues within 4Å: Chain C: T.113, T.114, G.181 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.114, C:T.114, C:G.181 Water bridges: C:A.115 GOL.32: 3 residues within 4Å: Chain D: T.113, T.114, G.181 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.113, D:T.114, D:G.181 Water bridges: D:A.115 GOL.40: 3 residues within 4Å: Chain E: T.113, T.114, G.181 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.113, E:T.114, E:G.181 Water bridges: E:A.115 GOL.48: 3 residues within 4Å: Chain F: T.113, T.114, G.181 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:T.113, F:T.114, F:G.181 Water bridges: F:A.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pisco, J.P. et al., Uncoupling conformational states from activity in an allosteric enzyme. Nat Commun (2017)

Release Date

2017-06-21

Peptides

ATP phosphoribosyltransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

ATP phosphoribosyltransferase

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