SMTL ID : 6njp.1

Structure of the assembled ATPase EscN in complex with its central stalk EscO from the enteropathogenic E. coli (EPEC) type III secretion system

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

ADP.1: 13 residues within 4Å: Chain A: S.368, R.369 Chain B: S.182, G.183, V.184, G.185, K.186, S.187, T.188, M.192, F.358 Ligands: MG.2, AF3.3 16 PLIP interactions: 4 interactions with chain A, 12 interactions with chain B Hydrogen bonds: A:R.369, B:G.183, B:V.184, B:G.185, B:K.186, B:S.187, B:S.187, B:T.188, B:T.188 Water bridges: A:R.369, B:R.210 Salt bridges: A:R.369, A:R.369, B:K.186 pi-Stacking: B:F.358, B:F.358 ADP.4: 14 residues within 4Å: Chain B: S.368, R.369 Chain C: S.182, G.183, V.184, G.185, K.186, S.187, T.188, F.358, P.359, T.431 Ligands: MG.5, AF3.6 16 PLIP interactions: 11 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:G.183, C:V.184, C:G.185, C:K.186, C:S.187, C:T.188, C:T.188, C:T.431, B:S.368 Salt bridges: C:K.186, B:R.369, B:R.369 pi-Stacking: C:F.358, C:F.358 Water bridges: B:R.369, B:R.369 ADP.7: 14 residues within 4Å: Chain C: S.368, R.369 Chain D: S.182, G.183, V.184, G.185, K.186, S.187, T.188, F.358, P.359, T.431 Ligands: MG.8, AF3.9 14 PLIP interactions: 3 interactions with chain C, 11 interactions with chain D Hydrogen bonds: C:S.368, D:G.183, D:V.184, D:K.186, D:S.187, D:T.188, D:T.188, D:T.431 Salt bridges: C:R.369, C:R.369, D:K.186 Water bridges: D:S.187 pi-Stacking: D:F.358, D:F.358 ADP.10: 12 residues within 4Å: Chain D: S.368, R.369 Chain E: G.183, V.184, G.185, K.186, S.187, T.188, F.358, T.431 Ligands: MG.11, AF3.12 16 PLIP interactions: 13 interactions with chain E, 3 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:T.431, D:S.368 Water bridges: E:K.186, 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: 4 residues within 4Å: Chain B: S.187, E.213 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: 5 residues within 4Å: Chain C: S.187, E.213, 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: 4 residues within 4Å: Chain D: S.187, E.213 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: 4 residues within 4Å: Chain E: S.187, R.210 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: 10 residues within 4Å: Chain A: R.339, S.340, R.369 Chain B: G.183, K.186, E.209, R.210, L.324 Ligands: ADP.1, MG.2 No protein-ligand interaction detected (PLIP) AF3.6: 11 residues within 4Å: Chain B: R.339, S.340, R.369 Chain C: S.182, G.183, K.186, E.209, R.210, L.324 Ligands: ADP.4, MG.5 No protein-ligand interaction detected (PLIP) AF3.9: 11 residues within 4Å: Chain C: R.339, S.340, R.369 Chain D: S.182, G.183, K.186, E.209, R.210, L.324 Ligands: ADP.7, MG.8 No protein-ligand interaction detected (PLIP) AF3.12: 10 residues within 4Å: Chain D: R.339, S.340, R.369 Chain E: G.183, 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
EscO: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Translocator EscN

EscO

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