Research workbench
Cytochrome c-type biogenesis protein CcmABCD from E. coli
Analyse Cytochrome c-type biogenesis protein CcmABCD from E. coli in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F02
- Type
- protein
- Length
- 1,130 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.24
- Source
- Escherichia coli BL21(DE3)
- Molecule
- Cytochrome c biogenesis ATP-binding export protein CcmA; Heme exporter protein B; Heme…
- EC
- 7.6.2.5
- UniProt
- P33931, P0ABL8, P0ABM1, P0ABM5
- Ligands
- 3PE, MG, PO4
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · resolution 3.24 · 4 distinct chains · 58% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Cytochrome c biogenesis ATP-binding export protein CcmA (EC 7.6.2.5) | protein | 202 | 27% helix, 19% strand | P33931 |
| B, F | Heme exporter protein B | protein | 220 | 75% helix, 0% strand | P0ABL8 |
| C | Heme exporter protein C | protein | 231 | 67% helix, 0% strand | P0ABM1 |
| D | Heme exporter protein D | protein | 55 | 65% helix, 0% strand | P0ABM5 |
Ligands and binding sites
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · chains B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, E
- PO4 · Phosphate ion · ion · 2 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 420 | 0.81 | 0.90 | 57 | empty |
| 2 | 234 | 0.81 | 0.94 | 39 | empty |
| 3 | 270 | 0.77 | 0.90 | 57 | empty |
| 4 | 509 | 0.71 | 0.80 | 51 | empty |
| 5 | 64 | 0.65 | 0.93 | 18 | empty |
Interfaces
11 interfaces between chains.
- B–F · 2015 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1438 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 1309 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1285 Ų buried · 14 hydrogen bonds · protein-protein
- C–F · 1030 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- P33931 · AlphaFold monomer V2.0 prediction for cytochrome C biogenesis ATP- binding export protein… · a predicted model of the same protein · chain A against A, TM-score 0.97
- P0ABL8 · AlphaFold monomer V2.0 prediction for heme exporter protein B (P0ABL8) · a predicted model of the same protein · chain F against A, TM-score 0.97
- P0ABM1 · AlphaFold monomer V2.0 prediction for heme exporter protein C (P0ABM1) · a predicted model of the same protein · chain C against A, TM-score 0.90
- P0ABM5 · AlphaFold monomer V2.0 prediction for heme exporter protein D (P0ABM5) · a predicted model of the same protein · chain D against A, TM-score 0.74
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P33931
- Every structure of UniProt P0ABL8
- Every structure of UniProt P0ABM1
- Every structure of UniProt P0ABM5
- Elsewhere: RCSB PDB 7F02 · PDBe 7F02 · UniProt P33931 · UniProt P0ABL8 · UniProt P0ABM1 · UniProt P0ABM5
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