SMTL ID : 5ybi.2 (1 other biounit)

Structure of the bacterial pathogens ATPase with substrate AMPPNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

monomer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: A.99, G.100, G.102, K.103, T.104, F.105 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.103, A:T.104, A:T.104 Water bridges: A:G.100, A:C.101 Salt bridges: A:K.103 SO4.2: 2 residues within 4Å: Chain A: R.161, R.191 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.191 Salt bridges: A:R.161, A:R.191 SO4.3: 5 residues within 4Å: Chain A: S.268, R.269, N.270, K.284 Ligands: MG.15 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.268, A:R.269, A:N.270 Water bridges: A:K.284, A:K.284, A:K.284 Salt bridges: A:K.284

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

MG.4: 6 residues within 4Å: Chain A: I.124, E.126, D.187, S.188, R.191, L.243 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.124, A:S.188, H2O.2 MG.5: 6 residues within 4Å: Chain A: S.114, G.115, A.116, Y.119, K.143, R.146 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:A.116 MG.6: 4 residues within 4Å: Chain A: I.280, D.281, S.282, L.346 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.280, H2O.1 MG.7: 4 residues within 4Å: Chain A: K.103, M.107, D.187, T.241 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.187, H2O.8 MG.8: 3 residues within 4Å: Chain A: H.20, M.21, D.58 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain A: R.55, P.56, N.59, A.170 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:P.56, H2O.7 MG.10: 4 residues within 4Å: Chain A: D.248, A.254, E.255, R.258 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.248 MG.11: 1 residues within 4Å: Chain A: E.133 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain A: T.104, N.108, E.133, T.134, Y.137 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Ligands: MG.20 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain A: E.112, H.113, S.114, K.143 No protein-ligand interaction detected (PLIP) MG.15: 6 residues within 4Å: Chain A: S.98, C.101, L.267, S.268, R.269 Ligands: SO4.3 No protein-ligand interaction detected (PLIP) MG.16: 6 residues within 4Å: Chain A: M.21, H.22, T.23, L.37, G.38, I.167 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain A: S.157, S.158 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain A: R.194, R.197 No protein-ligand interaction detected (PLIP) MG.19: 4 residues within 4Å: Chain A: V.159, C.162, N.163, Y.166 No protein-ligand interaction detected (PLIP) MG.20: 4 residues within 4Å: Chain A: T.153, D.155, Y.156 Ligands: MG.13 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.155, H2O.5 MG.21: 5 residues within 4Å: Chain A: Q.24, L.29, V.34, G.38, V.40 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.38, H2O.3 MG.22: 4 residues within 4Å: Chain A: L.308, E.311, L.315, K.338 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.311, H2O.6 MG.23: 3 residues within 4Å: Chain A: R.67, G.228, K.229 No protein-ligand interaction detected (PLIP) MG.24: 5 residues within 4Å: Chain A: F.217, L.220, P.221, E.256, I.260 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.217, A:E.256, H2O.6 MG.25: 2 residues within 4Å: Chain A: V.159, N.163 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, X. et al., Structural Insight Into Conformational Changes Induced by ATP Binding in a Type III Secretion-Associated ATPase FromShigella flexneri. Front Microbiol (2018)

Release Date

2018-06-20

Peptides

Probable ATP synthase SpaL/MxiB: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Probable ATP synthase SpaL/MxiB

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