SMTL ID : 4yb5.1

Adenosine triphosphate phosphoribosyltransferase from Campylobacter jejuni in complex with the allosteric inhibitor histidine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

homo-hexamer

Ligands

8 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.1: 5 residues within 4Å: Chain A: D.101, F.102, V.221, M.222, R.225 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.225 SCN.2: 4 residues within 4Å: Chain A: N.182 Chain F: P.112, P.160, R.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.182 SCN.6: 6 residues within 4Å: Chain B: L.100, D.101, F.102, V.221, M.222, R.225 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.225 SCN.9: 5 residues within 4Å: Chain C: D.101, F.102, V.221, M.222, R.225 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.225 SCN.16: 4 residues within 4Å: Chain E: D.101, F.102, M.222, R.225 No protein-ligand interaction detected (PLIP) SCN.17: 5 residues within 4Å: Chain C: P.112, P.160, R.161, L.183 Chain E: N.182 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.182 SCN.19: 5 residues within 4Å: Chain F: D.101, F.102, V.221, M.222, R.225 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:R.225 SCN.20: 2 residues within 4Å: Chain F: K.187, V.188 No protein-ligand interaction detected (PLIP)

5 x K: POTASSIUM ION(Non-covalent)

K.3: 3 residues within 4Å: Chain A: Q.179, N.182 Chain F: R.161 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain A Metal complexes: F:R.161, A:Q.179 K.5: 3 residues within 4Å: Chain A: R.161 Chain F: Q.179, N.182 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain F Metal complexes: A:R.161, F:Q.179 K.7: 3 residues within 4Å: Chain B: Q.179, N.182 Chain D: R.161 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Metal complexes: D:R.161, B:Q.179 K.11: 3 residues within 4Å: Chain C: Q.179, N.182 Chain E: R.161 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C Metal complexes: E:R.161, C:Q.179 K.13: 3 residues within 4Å: Chain C: R.161 Chain E: Q.179, N.182 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C Metal complexes: E:Q.179, C:R.161

6 x HIS: HISTIDINE(Non-covalent)

HIS.4: 14 residues within 4Å: Chain A: Y.229, G.248, V.249, E.250, R.251, T.253, H.267, M.268, V.269 Chain E: M.231, H.233, L.257, S.289, L.291 13 PLIP interactions: 1 Ligand-Ligand interactions, 9 interactions with chain A, 3 interactions with chain E Salt bridges: H.4, E:H.233 Hydrophobic interactions: A:Y.229 Hydrogen bonds: A:V.249, A:E.250, A:R.251, A:T.253, A:T.253, A:T.253, A:V.269, E:S.289 Water bridges: A:Y.229 pi-Cation interactions: E:H.233 HIS.8: 14 residues within 4Å: Chain B: Y.229, G.248, V.249, E.250, R.251, T.253, H.267, M.268, V.269 Chain C: M.231, H.233, L.257, S.289, L.291 14 PLIP interactions: 2 Ligand-Ligand interactions, 9 interactions with chain B, 3 interactions with chain C Hydrogen bonds: H.8, B:V.249, B:E.250, B:R.251, B:R.251, B:T.253, B:T.253, B:T.253, B:V.269, C:S.289 Salt bridges: H.8, C:H.233 Hydrophobic interactions: B:Y.229 pi-Cation interactions: C:H.233 HIS.12: 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 13 PLIP interactions: 1 Ligand-Ligand interactions, 9 interactions with chain C, 3 interactions with chain F Salt bridges: H.12, F:H.233 Hydrophobic interactions: C:Y.229 Hydrogen bonds: C:V.249, C:E.250, C:R.251, C:T.253, C:T.253, C:T.253, C:V.269, F:S.289 Water bridges: C:Y.229 pi-Cation interactions: F:H.233 HIS.15: 15 residues within 4Å: Chain A: M.231, 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 13 PLIP interactions: 9 interactions with chain D, 3 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: D:Y.229 Hydrogen bonds: D:V.249, D:E.250, D:R.251, D:T.253, D:T.253, D:T.253, D:V.269, A:S.289 Water bridges: D:Y.229 Salt bridges: A:H.233, H.15 pi-Cation interactions: A:H.233 HIS.18: 14 residues within 4Å: Chain D: M.231, H.233, L.257, S.289, L.291 Chain E: Y.229, G.248, V.249, E.250, R.251, T.253, H.267, M.268, V.269 12 PLIP interactions: 8 interactions with chain E, 3 interactions with chain D, 1 Ligand-Ligand interactions 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 Salt bridges: D:H.233, H.18 pi-Cation interactions: D:H.233 HIS.22: 14 residues within 4Å: Chain B: M.231, H.233, L.257, S.289, L.291 Chain F: Y.229, G.248, V.249, E.250, R.251, T.253, H.267, M.268, V.269 15 PLIP interactions: 2 Ligand-Ligand interactions, 10 interactions with chain F, 3 interactions with chain B Hydrogen bonds: H.22, 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 Salt bridges: H.22, B:H.233 Hydrophobic interactions: F:Y.229 Water bridges: F:Y.229 pi-Cation interactions: B:H.233

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.10: 10 residues within 4Å: Chain C: S.227, L.246, P.247, G.248, V.249, M.268, V.269, S.270, K.271, L.274 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.227, C:S.227, C:G.248, C:V.269

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

PEG.14: 7 residues within 4Å: Chain D: K.236, P.256, L.257, D.260, E.261, N.263, V.264 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.236, D:L.257, D:N.263 PEG.21: 9 residues within 4Å: Chain F: V.221, A.224, R.225, E.226, S.227, K.228, P.294, I.295, E.296 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:E.226, F:K.228, F:I.295, F:E.296

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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