SMTL ID : 5ybi.1 (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

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

SO4.1: 5 residues within 4Å: Chain A: Y.266, S.268, R.269, N.270, K.284 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.266, A:S.268, A:R.269, A:N.270 Salt bridges: A:R.269, A:K.284 SO4.2: 3 residues within 4Å: Chain A: R.161, R.191, R.194 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.191, A:R.191 Salt bridges: A:R.161, A:R.191, A:R.194 SO4.3: 3 residues within 4Å: Chain A: S.19, H.20, H.22 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.20, A:H.22 SO4.4: 3 residues within 4Å: Chain A: D.295, E.296, R.299 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.296 Salt bridges: A:R.299

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.5: 16 residues within 4Å: Chain A: A.99, G.100, C.101, G.102, K.103, T.104, F.105, M.109, E.130, F.277, P.278, Q.348, D.349, Y.350 Ligands: MG.6, MG.12 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.100, A:C.101, A:G.102, A:K.103, A:K.103, A:T.104, A:T.104, A:T.104, A:T.104, A:F.105, A:E.130, A:E.130, A:Q.348, A:Y.350 Water bridges: A:A.99 pi-Stacking: A:F.277

16 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain A: K.103, T.104 Ligands: ANP.5 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.104, H2O.4 MG.7: 2 residues within 4Å: Chain A: D.262, R.288 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain A: S.157, S.158 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain A: L.352, G.353 No protein-ligand interaction detected (PLIP) MG.10: 6 residues within 4Å: Chain A: R.67, A.68, I.70, G.90, G.228, K.229 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain A: A.68, A.69, K.231 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain A: L.106, M.109, P.278, Q.348 Ligands: ANP.5 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain A: L.75, T.355, Y.356, E.357 No protein-ligand interaction detected (PLIP) MG.14: 5 residues within 4Å: Chain A: T.23, Q.24, L.29, V.34, G.38 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.38, H2O.2 MG.15: 4 residues within 4Å: Chain A: L.84, L.85, S.282, R.306 No protein-ligand interaction detected (PLIP) MG.16: 5 residues within 4Å: Chain A: T.104, M.107, N.108, L.123, T.134 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain A: A.208, V.214 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain A: Q.348, D.349, L.352 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain A: R.127, R.129, E.130 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain A: D.155, Y.156 No protein-ligand interaction detected (PLIP) MG.21: 5 residues within 4Å: Chain A: V.25, G.26, I.171, F.174, F.175 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:I.171

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
A

Probable ATP synthase SpaL/MxiB

Related Entries With Identical Sequence