Research workbench
Crystal structure of oxidized cytochrome C6A from arabidopsis thaliana
Analyse Crystal structure of oxidized cytochrome C6A from arabidopsis thaliana in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DGE
- Type
- protein
- Length
- 406 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C6
- UniProt
- Q93VA3
- Ligands
- HEM, ZN
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Cytochrome C6 | protein | 102 | 56% helix, 4% strand | Q93VA3 |
| D | Cytochrome C6 | protein | 100 | 56% helix, 4% strand | Q93VA3 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.83 | 0.84 | 76 | empty |
| 2 | 223 | 0.72 | 0.87 | 31 | HEM |
| 3 | 205 | 0.71 | 0.87 | 28 | HEM |
| 4 | 225 | 0.70 | 0.86 | 27 | HEM |
| 5 | 204 | 0.68 | 0.85 | 26 | HEM |
Interfaces
6 interfaces between chains.
- B–D · 540 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 525 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 362 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 346 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 88 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 4 disulfide (heme attachment, disulfide).
Compared structures
- 2DGE · Crystal structure of oxidized cytochrome C6A from Arabidopsis thaliana · the same entry in another collection · chain C against C, TM-score 1.00
- Q93VA3 · AlphaFold monomer V2.0 prediction for cytochrome C6, chloroplastic (Q93VA3) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 Q93VA3
- Elsewhere: RCSB PDB 2DGE · PDBe 2DGE · UniProt Q93VA3
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