SMTL ID : 7vfp.1

Cytochrome c-type biogenesis protein CcmABCD from E. coli in complex with heme and single ATP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-1-1-mer

Ligands

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 11 residues within 4Å: Chain C: H.60, A.64, I.65, M.68, G.111, W.114, R.128, E.132, Q.191, Q.192, I.194 8 PLIP interactions: 8 interactions with chain C, Hydrophobic interactions: C:A.64, C:I.65, C:W.114, C:W.114, C:R.128, C:Q.192, C:I.194 pi-Stacking: C:H.60

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain E: T.43, H.83 Ligands: ATP.3 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:T.43, E:H.83, H2O.1, H2O.1

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.3: 12 residues within 4Å: Chain E: R.13, R.16, L.18, N.38, G.39, A.40, G.41, K.42, T.43, T.44, H.83 Ligands: MG.2 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:R.13, E:R.16, E:N.38, E:G.39, E:T.43, E:T.44 Salt bridges: E:K.42, E:K.42, E:H.83 pi-Cation interactions: E:R.13, E:R.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, J. et al., Structures of the CcmABCD heme release complex at multiple states. Nat Commun (2022)

Release Date

2022-11-09

Peptides

Cytochrome c biogenesis ATP-binding export protein CcmA: AE
Heme exporter protein B: BF
Heme exporter protein C: C
Heme exporter protein D: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Cytochrome c biogenesis ATP-binding export protein CcmA

Heme exporter protein B

Heme exporter protein C

Heme exporter protein D

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