Research workbench
Crystal structure of the outer membrane decaheme cytochrome omca
Analyse Crystal structure of the outer membrane decaheme cytochrome omca in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LMH
- Type
- protein
- Length
- 2,774 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular iron oxide respiratory system surface decaheme cytochrome C component omca
- UniProt
- Q8EG33
- Ligands
- HEC, CA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Extracellular iron oxide respiratory system surface decaheme cytochrome C component omca | protein | 693 | 20% helix, 27% strand | Q8EG33 |
| B | Extracellular iron oxide respiratory system surface decaheme cytochrome C component omca | protein | 694 | 20% helix, 28% strand | Q8EG33 |
| C | Extracellular iron oxide respiratory system surface decaheme cytochrome C component omca | protein | 692 | 20% helix, 27% strand | Q8EG33 |
| D | Extracellular iron oxide respiratory system surface decaheme cytochrome C component omca | protein | 695 | 20% helix, 26% strand | Q8EG33 |
Ligands and binding sites
- HEC · Heme C · ligand · 40 copies · chains A, B, C, D
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 16 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 753 | 0.87 | 0.91 | 114 | HEC |
| 2 | 707 | 0.87 | 0.91 | 111 | HEC |
| 3 | 675 | 0.86 | 0.91 | 106 | HEC |
| 4 | 665 | 0.86 | 0.90 | 96 | HEC |
| 5 | 566 | 0.84 | 0.89 | 73 | HEC |
Interfaces
3 interfaces between chains.
- B–C · 617 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 552 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 545 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 79 cofactor, 8 disulfide (heme c attachment, disulfide).
Compared structures
- 4LMH · Crystal structure of the outer membrane decaheme cytochrome OmcA · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8EG33
- Elsewhere: RCSB PDB 4LMH · PDBe 4LMH · UniProt Q8EG33
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