SMTL ID : 6zxq.1

Adenylosuccinate Synthetase from H. pylori in complex with HDA, GDP, IMO, Mg

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

2 x HDA: HADACIDIN(Non-covalent)

HDA.1: 14 residues within 4Å: Chain A: D.12, N.37, G.39, T.121, V.264, G.289, T.290, T.291, T.292, R.294, R.296 Ligands: GDP.2, IMO.3, MG.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.12, A:G.39, A:T.290, A:T.290, A:T.291, A:T.291, A:T.292, A:R.296 Salt bridges: A:R.294 HDA.5: 14 residues within 4Å: Chain B: D.12, N.37, G.39, T.121, V.264, G.289, T.290, T.291, T.292, R.294, R.296 Ligands: GDP.6, IMO.7, MG.8 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.12, B:G.39, B:T.290, B:T.291, B:T.292, B:R.296 Salt bridges: B:R.294

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.2: 22 residues within 4Å: Chain A: D.12, E.13, G.14, K.15, G.16, K.17, G.39, H.40, T.41, T.290, R.296, M.321, K.322, D.324, V.325, S.400, T.401, S.402, P.403 Ligands: HDA.1, IMO.3, MG.4 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:D.12, A:D.12, A:E.13, A:G.14, A:K.15, A:G.16, A:T.41, A:T.41, A:K.322, A:S.400, A:S.402 Water bridges: A:K.17, A:T.41, A:G.285, A:G.285, A:A.286, A:F.288, A:T.290, A:T.290, A:R.296, A:K.322, A:K.322 Salt bridges: A:K.15, A:H.40, A:R.296, A:D.324 GDP.6: 22 residues within 4Å: Chain B: D.12, E.13, G.14, K.15, G.16, K.17, G.39, H.40, T.41, T.290, R.296, M.321, K.322, D.324, V.325, S.400, T.401, S.402, P.403 Ligands: HDA.5, IMO.7, MG.8 28 PLIP interactions: 28 interactions with chain B Hydrogen bonds: B:D.12, B:E.13, B:E.13, B:G.14, B:K.15, B:G.16, B:T.41, B:T.41, B:T.290, B:K.322, B:S.400, B:S.402 Water bridges: B:K.17, B:T.41, B:G.285, B:G.285, B:A.286, B:F.288, B:T.290, B:T.290, B:R.296, B:K.322, B:K.322, B:D.324 Salt bridges: B:K.15, B:H.40, B:R.296, B:D.324

2 x IMO: 6-O-PHOSPHORYL INOSINE MONOPHOSPHATE(Non-covalent)

IMO.3: 23 residues within 4Å: Chain A: W.10, G.11, D.12, K.15, N.37, A.38, G.39, H.40, G.119, T.120, T.121, A.214, Q.215, L.219, V.229, T.230, V.264, G.265, R.294 Chain B: R.135 Ligands: HDA.1, GDP.2, MG.4 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.12, A:N.37, A:G.39, A:T.121, A:Q.215, A:Q.215, A:V.264, A:R.294, A:R.294 Water bridges: A:K.123, A:I.125, A:G.126, A:G.126, A:T.230, A:S.231, A:R.263, A:N.266 Salt bridges: A:K.15, A:H.40, B:R.135 IMO.7: 23 residues within 4Å: Chain A: R.135 Chain B: W.10, G.11, D.12, K.15, N.37, A.38, G.39, H.40, G.119, T.120, T.121, A.214, Q.215, L.219, V.229, T.230, V.264, G.265, R.294 Ligands: HDA.5, GDP.6, MG.8 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.12, B:N.37, B:G.39, B:T.121, B:Q.215, B:Q.215, B:T.230, B:V.264, B:R.294, B:R.294 Water bridges: B:T.121, B:K.123, B:G.126, B:G.126, B:T.230, B:S.231, B:R.263, B:N.266 Salt bridges: B:K.15, B:H.40, A:R.135

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: D.12, G.39, T.290 Ligands: HDA.1, GDP.2, IMO.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.12, A:G.39, HDA.1 MG.8: 6 residues within 4Å: Chain B: D.12, G.39, T.290 Ligands: HDA.5, GDP.6, IMO.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.12, B:G.39, HDA.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bubic, A. et al., The pursuit of new alternative ways to eradicate Helicobacter pylori continues: Detailed characterization of interactions in the adenylosuccinate synthetase active site. Int.J.Biol.Macromol. (2023)

Release Date

2021-08-11

Peptides

Adenylosuccinate synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Adenylosuccinate synthetase