SMTL ID : 7kzz.1

Cryo-EM structure of YiiP-Fab complex in Holo state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.234, D.235, H.250, H.285, D.287 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.234, A:H.250, A:D.287 ZN.2: 4 residues within 4Å: Chain A: D.70, D.72, H.73, H.77 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.70, A:D.70, A:H.73, A:H.77 ZN.3: 6 residues within 4Å: Chain A: D.47, S.48, D.51, H.155, D.159, L.162 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.47, A:D.47, A:D.51, A:H.155, A:D.159 ZN.4: 4 residues within 4Å: Chain A: H.263, D.267 Chain D: H.285, D.287 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Metal complexes: D:H.285, D:D.287, A:H.263, A:D.267, A:D.267 ZN.5: 4 residues within 4Å: Chain A: H.285, D.287 Chain D: H.263, D.267 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Metal complexes: D:H.263, D:D.267, D:D.267, A:H.285, A:D.287 ZN.6: 5 residues within 4Å: Chain D: H.234, D.235, H.250, H.285, D.287 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.234, D:H.250, D:D.287 ZN.7: 4 residues within 4Å: Chain D: D.70, D.72, H.73, H.77 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.70, D:D.70, D:D.72, D:H.73, D:H.77 ZN.8: 6 residues within 4Å: Chain D: D.47, S.48, D.51, H.155, D.159, L.162 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.47, D:D.47, D:D.51, D:H.155, D:D.159

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lopez-Redondo, M. et al., Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP. J.Gen.Physiol. (2021)

Release Date

2021-01-06

Peptides

Cadmium and zinc efflux pump FieF: AD
Fab2R light chain: BE
Fab2R heavy chain: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

D
A

B
E

E
C

C
F

F
D

Membrane

We predict this structure to be a membrane protein.
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Cadmium and zinc efflux pump FieF

Fab2R light chain

Fab2R heavy chain

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