SMTL ID : 7f04.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-1-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.43, H.83, D.153 Ligands: ATP.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.5: 5 residues within 4Å: Chain A: A.131 Chain E: T.43, H.83, D.153 Ligands: ATP.6 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 ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 22 residues within 4Å: Chain A: R.13, R.16, L.18, N.38, G.39, A.40, G.41, K.42, T.43, T.44, H.83, E.154, H.186 Chain E: N.127, Q.128, L.129, S.130, A.131, G.132, Q.133, A.158 Ligands: MG.1 18 PLIP interactions: 14 interactions with chain A, 4 interactions with chain E Hydrogen bonds: A:R.16, A:G.39, A:G.39, A:K.42, A:T.43, A:T.43, A:T.44, A:T.44, A:E.154, E:S.130, E:A.131, E:G.132, E:A.158 Salt bridges: A:K.42, A:K.42, A:H.83, A:H.186 pi-Cation interactions: A:R.13 ATP.6: 21 residues within 4Å: Chain A: 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.5 19 PLIP interactions: 14 interactions with chain E, 5 interactions with chain A Hydrogen bonds: E:R.13, E:R.16, E:N.38, E:G.39, E:K.42, E:T.43, E:T.44, E:E.154, A:S.130, A:A.131, A:G.132, A:Q.133, A:A.158 Salt bridges: E:K.42, E:K.42, E:H.83, E:H.186 pi-Cation interactions: E:R.13, E:R.13

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

HEM.3: 13 residues within 4Å: Chain C: Q.50, H.60, V.61, A.64, G.111, S.112, W.114, G.115, M.118, W.119, R.128, L.129, E.132 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:V.61, C:A.64, C:W.114, C:W.114, C:W.114, C:W.119, C:W.119, C:R.128, C:E.132 pi-Stacking: C:H.60 pi-Cation interactions: C:R.128 Metal complexes: C:H.60

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

3PE.4: 12 residues within 4Å: Chain B: L.114 Chain C: P.98, A.101, F.105, I.143, H.147, R.220 Chain D: P.31, V.34, L.35, H.38, Q.42 14 PLIP interactions: 9 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:P.98, C:A.101, C:F.105, C:F.105, C:F.105, D:P.31 Hydrogen bonds: C:H.147, D:Q.42, D:Q.42 Salt bridges: C:H.147, C:H.147, C:R.220, D:H.38, D:H.38

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.
Show / Hide

Cytochrome c biogenesis ATP-binding export protein CcmA

Heme exporter protein B

Heme exporter protein C

Heme exporter protein D

Related Entries With Identical Sequence