Research workbench
Dihydro-heme D1 dehydrogenase nirn in complex with dhe
Analyse Dihydro-heme D1 dehydrogenase nirn in complex with dhe in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RTE
- Type
- protein
- Length
- 930 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C
- EC
- 1.7.2.1
- UniProt
- A0A0C7D2F2
- Ligands
- HEC
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C (EC 1.7.2.1) | protein | 464 | 14% helix, 42% strand | A0A0C7D2F2 |
| B | Cytochrome C (EC 1.7.2.1) | protein | 466 | 13% helix, 42% strand | A0A0C7D2F2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 782 | 0.76 | 0.80 | 68 | empty |
| 2 | 766 | 0.76 | 0.80 | 71 | empty |
| 3 | 231 | 0.69 | 0.85 | 41 | HEC |
| 4 | 199 | 0.68 | 0.86 | 36 | HEC |
| 5 | 422 | 0.65 | 0.78 | 47 | empty |
Interfaces
1 interface between chains.
- A–B · 710 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme c attachment).
Compared structures
- 6RTE · Dihydro-heme d1 dehydrogenase NirN in complex with DHE · 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 A0A0C7D2F2
- Elsewhere: RCSB PDB 6RTE · PDBe 6RTE · UniProt A0A0C7D2F2
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