SMTL ID : 4yb6.1

Adenosine triphosphate phosphoribosyltransferase from Campylobacter jejuni in complex with the inhibitors AMP and histidine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-hexamer

Ligands

6 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 11 residues within 4Å: Chain A: G.103, C.105, D.170, L.171, V.172, S.173, S.174, G.175, A.176, T.177 Chain D: H.34 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:G.103, A:D.170, A:S.173, A:S.174, A:S.174, A:S.174, A:G.175, A:A.176, A:T.177, A:T.177 Water bridges: A:N.76, A:N.76, A:S.174, A:S.174, A:L.178 Salt bridges: D:H.34 AMP.5: 10 residues within 4Å: Chain B: L.18, C.105, D.170, L.171, V.172, S.173, S.174, G.175, A.176, T.177 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:G.103, B:L.171, B:L.171, B:S.173, B:S.174, B:S.174, B:S.174, B:G.175, B:A.176, B:T.177, B:T.177, B:T.177 Water bridges: B:Y.132, B:L.178 AMP.9: 10 residues within 4Å: Chain C: G.103, C.105, D.170, L.171, V.172, S.173, S.174, G.175, A.176, T.177 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:G.103, C:L.171, C:L.171, C:S.173, C:S.174, C:S.174, C:S.174, C:G.175, C:A.176, C:T.177, C:T.177, C:T.177 Water bridges: C:S.173, C:S.173, C:S.174, C:S.174, C:L.178 AMP.14: 10 residues within 4Å: Chain D: G.103, C.105, D.170, L.171, V.172, S.173, S.174, G.175, A.176, T.177 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:G.103, D:L.171, D:L.171, D:S.173, D:S.174, D:S.174, D:S.174, D:G.175, D:A.176, D:T.177, D:T.177, D:T.177 Water bridges: D:L.178 AMP.18: 11 residues within 4Å: Chain E: G.103, C.105, D.170, L.171, V.172, S.173, S.174, G.175, A.176, T.177 Ligands: MG.23 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:G.103, E:L.171, E:L.171, E:S.173, E:S.174, E:S.174, E:S.174, E:G.175, E:A.176, E:T.177, E:T.177, E:T.177 Water bridges: E:N.76, E:N.76, E:D.170, E:S.173, E:L.178 AMP.24: 9 residues within 4Å: Chain F: C.105, D.170, L.171, V.172, S.173, S.174, G.175, A.176, T.177 19 PLIP interactions: 19 interactions with chain F Hydrogen bonds: F:G.103, F:L.171, F:L.171, F:S.173, F:S.174, F:S.174, F:S.174, F:G.175, F:A.176, F:T.177, F:T.177, F:T.177 Water bridges: F:N.76, F:N.76, F:S.173, F:S.173, F:S.174, F:S.174, F:L.178

6 x HIS: HISTIDINE(Non-covalent)

HIS.2: 16 residues within 4Å: Chain A: Y.229, G.248, V.249, E.250, R.251, P.252, T.253, H.267, M.268, V.269 Chain E: M.231, L.232, H.233, L.257, S.289, L.291 12 PLIP interactions: 8 interactions with chain A, 3 interactions with chain E, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.229 Hydrogen bonds: A:V.249, A:E.250, A:R.251, A:T.253, A:T.253, A:V.269, E:S.289 Water bridges: A:Y.229 Salt bridges: E:H.233, H.2 pi-Cation interactions: E:H.233 HIS.6: 15 residues within 4Å: Chain B: Y.229, G.248, V.249, E.250, R.251, P.252, T.253, H.267, M.268, V.269 Chain C: M.231, H.233, L.257, S.289, L.291 14 PLIP interactions: 9 interactions with chain B, 3 interactions with chain C, 2 Ligand-Ligand interactions Hydrophobic interactions: B:Y.229 Hydrogen bonds: B:V.249, B:E.250, B:R.251, B:R.251, B:R.251, B:T.253, B:T.253, B:V.269, C:S.289, H.6 Salt bridges: C:H.233, H.6 pi-Cation interactions: C:H.233 HIS.10: 16 residues within 4Å: Chain C: Y.229, G.248, V.249, E.250, R.251, P.252, T.253, H.267, M.268, V.269 Chain F: M.231, L.232, H.233, L.257, S.289, L.291 15 PLIP interactions: 10 interactions with chain C, 3 interactions with chain F, 2 Ligand-Ligand interactions Hydrophobic interactions: C:Y.229 Hydrogen bonds: C:V.249, C:E.250, C:R.251, C:R.251, C:T.253, C:T.253, C:T.253, C:V.269, F:S.289, H.10 Water bridges: C:Y.229 Salt bridges: F:H.233, H.10 pi-Cation interactions: F:H.233 HIS.15: 16 residues within 4Å: Chain A: M.231, L.232, H.233, L.257, S.289, L.291 Chain D: Y.229, G.248, V.249, E.250, R.251, P.252, T.253, H.267, M.268, V.269 12 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain A, 8 interactions with chain D Salt bridges: H.15, A:H.233 Hydrogen bonds: A:S.289, D:V.249, D:E.250, D:R.251, D:T.253, D:T.253, D:T.253, D:V.269 pi-Cation interactions: A:H.233 Hydrophobic interactions: D:Y.229 HIS.19: 16 residues within 4Å: Chain D: M.231, L.232, H.233, L.257, S.289, L.291 Chain E: Y.229, G.248, V.249, E.250, R.251, P.252, T.253, H.267, M.268, V.269 13 PLIP interactions: 9 interactions with chain E, 1 Ligand-Ligand interactions, 3 interactions with chain D Hydrophobic interactions: E:Y.229 Hydrogen bonds: E:V.249, E:E.250, E:R.251, E:T.253, E:T.253, E:T.253, E:V.269, D:S.289 Water bridges: E:Y.229 Salt bridges: H.19, D:H.233 pi-Cation interactions: D:H.233 HIS.25: 16 residues within 4Å: Chain B: M.231, L.232, H.233, L.257, S.289, L.291 Chain F: Y.229, G.248, V.249, E.250, R.251, P.252, T.253, H.267, M.268, V.269 14 PLIP interactions: 9 interactions with chain F, 3 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: F:Y.229 Hydrogen bonds: F:V.249, F:E.250, F:R.251, F:R.251, F:T.253, F:T.253, F:T.253, F:V.269, B:S.289, H.25 Salt bridges: B:H.233, H.25 pi-Cation interactions: B:H.233

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 4 residues within 4Å: Chain A: R.106, E.185, V.186, V.188 No protein-ligand interaction detected (PLIP) PEG.7: 3 residues within 4Å: Chain B: R.106, V.186, V.188 No protein-ligand interaction detected (PLIP) PEG.11: 3 residues within 4Å: Chain C: R.106, E.185, V.186 No protein-ligand interaction detected (PLIP) PEG.16: 3 residues within 4Å: Chain D: R.106, E.185, V.186 1 PLIP interactions: 1 interactions with chain D Water bridges: D:V.188 PEG.20: 4 residues within 4Å: Chain E: R.106, E.185, V.186, V.188 1 PLIP interactions: 1 interactions with chain E Water bridges: E:V.188 PEG.26: 4 residues within 4Å: Chain F: R.106, E.185, V.186, V.188 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.106 Water bridges: F:V.188

9 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.4: 3 residues within 4Å: Chain A: D.57, N.81, E.84 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.57, H2O.5, H2O.5, H2O.5, H2O.5, H2O.5 MG.8: 2 residues within 4Å: Chain B: D.57, E.84 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.57, H2O.7, H2O.9 MG.12: 3 residues within 4Å: Chain C: D.57, N.81, E.84 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.57, H2O.14, H2O.14, H2O.14, H2O.14 MG.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain D: D.57, E.84 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:D.57, H2O.19, H2O.19, H2O.19, H2O.19, H2O.19 MG.21: 2 residues within 4Å: Chain E: D.57, E.84 6 PLIP interactions: 1 interactions with chain E, 5 Ligand-Water interactions Metal complexes: E:D.57, H2O.23, H2O.23, H2O.23, H2O.23, H2O.23 MG.22: 5 residues within 4Å: Chain E: A.224, E.226, S.227, K.228, I.295 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:S.227, H2O.20, H2O.22, H2O.23 MG.23: 1 residues within 4Å: Ligands: AMP.18 No protein-ligand interaction detected (PLIP) MG.27: 2 residues within 4Å: Chain F: D.57, E.84 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.57, H2O.27, H2O.27, H2O.27

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mittelstadt, G. et al., Campylobacter jejuni adenosine triphosphate phosphoribosyltransferase is an active hexamer that is allosterically controlled by the twisting of a regulatory tail. Protein Sci. (2016)

Release Date

2016-03-09

Peptides

ATP phosphoribosyltransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

ATP phosphoribosyltransferase

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