Research workbench
Crystal structure of mtrc from shewanella baltica OS185
Analyse Crystal structure of mtrc from shewanella baltica OS185 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QYC
- Type
- protein
- Length
- 1,817 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Decaheme C-type cytochrome, OMCA/MTRC family
- Ligands
- HEC, CA
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Decaheme C-type cytochrome, OMCA/MTRC family | protein | 605 | 23% helix, 27% strand | — |
| B | Decaheme C-type cytochrome, OMCA/MTRC family | protein | 608 | 23% helix, 27% strand | — |
| C | Decaheme C-type cytochrome, OMCA/MTRC family | protein | 604 | 24% helix, 27% strand | — |
Ligands and binding sites
- HEC · Heme C · ligand · 30 copies · chains A, B, C
- CA · Calcium ion · metal · 8 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.87 | 0.88 | 102 | HEC |
| 2 | 999 | 0.87 | 0.88 | 102 | HEC |
| 3 | 1196 | 0.86 | 0.87 | 106 | HEC |
| 4 | 741 | 0.84 | 0.87 | 81 | HEC |
| 5 | 890 | 0.83 | 0.85 | 97 | HEC |
Interfaces
3 interfaces between chains.
- A–B · 1017 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 926 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 865 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 cofactor, 6 disulfide (heme c attachment, disulfide).
Compared structures
- 6QYC · Crystal structure of MtrC from Shewanella baltica OS185 · 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
- Elsewhere: RCSB PDB 6QYC · PDBe 6QYC
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