Research workbench
Crystal structure of Cytochrome CL from the marine methylotrophic bacterium Methylophaga aminisulfidivorans MPT (Ma-CytcL)
Analyse Crystal structure of Cytochrome CL from the marine methylotrophic bacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C90
- Type
- protein
- Length
- 597 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.13
- Source
- Methylophaga aminisulfidivorans MP
- Molecule
- Cytochrome c, mono-and diheme variant
- UniProt
- F5SWR8
- Ligands
- HEC, NA, CA, FE
- Pockets
- 7 · best druggability 0.91
Structure
x-ray diffraction · resolution 2.13 · 3 distinct chains · 45% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytochrome c, mono-and diheme variant | protein | 151 | 46% helix, 1% strand | F5SWR8 |
| C | Cytochrome c, mono-and diheme variant | protein | 145 | 46% helix, 1% strand | F5SWR8 |
| D | Cytochrome c, mono-and diheme variant | protein | 150 | 44% helix, 1% strand | F5SWR8 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B, D, C
- NA · Sodium ion · metal · 8 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1088 | 0.91 | 0.94 | 154 | HEC, NA |
| 2 | 117 | 0.45 | 0.78 | 23 | empty |
| 3 | 124 | 0.44 | 0.77 | 23 | empty |
| 4 | 110 | 0.37 | 0.74 | 26 | empty |
| 5 | 97 | 0.37 | 0.75 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 696 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 636 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 611 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 601 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 80 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (heme c attachment).
Compared structures
- 7C90 · Crystal structure of cytochrome cl from the marine methylotrophic bacterium methylophaga… · 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 F5SWR8
- Elsewhere: RCSB PDB 7C90 · PDBe 7C90 · UniProt F5SWR8
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