SMTL ID : 6njo.1

Structure of the assembled ATPase EscN from the enteropathogenic E. coli (EPEC) type III secretion system

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 14 residues within 4Å: Chain A: R.369 Chain B: S.182, G.183, V.184, G.185, K.186, S.187, T.188, M.192, F.358, P.359, T.431 Ligands: MG.2, AF3.3 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.183, B:V.184, B:G.185, B:K.186, B:S.187, B:T.188, B:T.188 Water bridges: B:K.186, B:R.210, A:R.369 Salt bridges: B:K.186, A:R.369, A:R.369 pi-Stacking: B:F.358, B:F.358 ADP.4: 12 residues within 4Å: Chain B: R.369 Chain C: S.182, G.183, V.184, G.185, K.186, S.187, T.188, F.358, T.431 Ligands: MG.5, AF3.6 16 PLIP interactions: 2 interactions with chain B, 14 interactions with chain C Salt bridges: B:R.369, B:R.369, C:K.186 Hydrogen bonds: C:G.183, C:V.184, C:G.185, C:K.186, C:S.187, C:T.188, C:T.188, C:Q.429, C:T.431 Water bridges: C:S.187, C:S.270 pi-Stacking: C:F.358, C:F.358 ADP.7: 13 residues within 4Å: Chain C: S.368, R.369 Chain D: G.183, V.184, G.185, K.186, S.187, T.188, F.358, P.359, T.431 Ligands: MG.8, AF3.9 15 PLIP interactions: 13 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.183, D:V.184, D:G.185, D:K.186, D:S.187, D:T.188, D:T.188, D:T.431 Water bridges: D:R.210, D:E.213 Salt bridges: D:K.186, C:R.369, C:R.369 pi-Stacking: D:F.358, D:F.358 ADP.10: 15 residues within 4Å: Chain D: S.368, R.369 Chain E: G.183, V.184, G.185, K.186, S.187, T.188, M.192, R.210, F.358, P.359, T.431 Ligands: MG.11, AF3.12 14 PLIP interactions: 12 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:G.183, E:V.184, E:G.185, E:K.186, E:S.187, E:T.188, E:T.188, E:R.210 Water bridges: E:R.210 Salt bridges: E:K.186, D:R.369, D:R.369 pi-Stacking: E:F.358, E:F.358

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain B: S.187, E.213, D.269 Ligands: ADP.1, AF3.3 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.187, H2O.1, H2O.1 MG.5: 4 residues within 4Å: Chain C: S.187, D.269 Ligands: ADP.4, AF3.6 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.187, H2O.1, H2O.1 MG.8: 6 residues within 4Å: Chain D: S.187, E.209, E.213, D.269 Ligands: ADP.7, AF3.9 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.187, H2O.1, H2O.1 MG.11: 6 residues within 4Å: Chain E: S.187, E.209, E.213, D.269 Ligands: ADP.10, AF3.12 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:S.187, H2O.1, H2O.1

4 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.3: 9 residues within 4Å: Chain A: S.340, R.369 Chain B: S.182, K.186, E.209, R.210, L.324 Ligands: ADP.1, MG.2 No protein-ligand interaction detected (PLIP) AF3.6: 9 residues within 4Å: Chain B: S.340, R.369 Chain C: G.183, K.186, E.209, R.210, L.324 Ligands: ADP.4, MG.5 No protein-ligand interaction detected (PLIP) AF3.9: 9 residues within 4Å: Chain C: S.340, R.369 Chain D: G.183, K.186, E.209, R.210, L.324 Ligands: ADP.7, MG.8 No protein-ligand interaction detected (PLIP) AF3.12: 9 residues within 4Å: Chain D: R.339, S.340, R.369 Chain E: K.186, E.209, R.210, L.324 Ligands: ADP.10, MG.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Majewski, D.D. et al., Cryo-EM structure of the homohexameric T3SS ATPase-central stalk complex reveals rotary ATPase-like asymmetry. Nat Commun (2019)

Release Date

2019-02-20

Peptides

Translocator EscN: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Translocator EscN

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