SMTL ID : 7f03.1

Cytochrome c-type biogenesis protein CcmABCD from E. coli in complex with ANP

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-1-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: T.43, H.83 Ligands: ANP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.43, A:H.83, H2O.1, H2O.1 MG.4: 4 residues within 4Å: Chain E: T.43, H.83, D.153 Ligands: ANP.5 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:T.43, E:H.83, H2O.1, H2O.1

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

ANP.2: 20 residues within 4Å: Chain A: R.13, R.16, L.18, S.37, N.38, G.39, A.40, K.42, T.43, T.44, H.83, H.186 Chain B: K.155 Chain E: Q.128, L.129, S.130, A.131, G.132, Q.133 Ligands: MG.1 18 PLIP interactions: 13 interactions with chain A, 4 interactions with chain E, 1 interactions with chain B Hydrogen bonds: A:R.16, A:G.39, A:G.39, A:K.42, A:K.42, A:K.42, A:T.43, A:T.43, A:T.44, A:T.44, A:H.186, E:S.130, E:A.131, E:G.132, E:Q.133, B:K.155 pi-Cation interactions: A:R.13, A:R.13 ANP.5: 22 residues within 4Å: Chain A: F.121, Q.128, S.130, A.131, G.132, Q.133, A.158 Chain E: R.13, R.16, L.18, S.37, N.38, G.39, A.40, G.41, K.42, T.43, T.44, H.83, E.154, H.186 Ligands: MG.4 18 PLIP interactions: 13 interactions with chain E, 5 interactions with chain A Hydrogen bonds: E:R.16, E:N.38, E:G.39, E:K.42, E:K.42, E:K.42, E:T.43, E:T.43, E:T.44, E:E.154, E:H.186, A:S.130, A:S.130, A:A.131, A:G.132, A:Q.133 pi-Cation interactions: E:R.13, E:R.13

1 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.3: 14 residues within 4Å: Chain B: H.17, A.19, L.114, M.117 Chain C: A.101, F.105, I.143, H.147, R.220 Chain D: I.30, V.34, L.35, H.38, Q.42 11 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: C:A.101, C:F.105, C:I.143, B:L.114, D:I.30 Salt bridges: C:H.147, C:H.147, C:R.220, D:H.38, D:H.38 Hydrogen bonds: D:Q.42

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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