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
- 6RTD
- Type
- protein
- Length
- 931 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
- DHE, HEC
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C (EC 1.7.2.1) | protein | 465 | 13% helix, 40% strand | A0A0C7D2F2 |
| B | Cytochrome C (EC 1.7.2.1) | protein | 466 | 13% helix, 40% strand | A0A0C7D2F2 |
Ligands and binding sites
- DHE · Heme D · ligand · 2 copies · chains A, B
- HEC · Heme C · ligand · 2 copies · chains A, B
- BU3 · (R,R)-2,3-butanediol · additive · chains A, B
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 | 1034 | 0.82 | 0.83 | 105 | DHE, HEC |
| 2 | 1133 | 0.81 | 0.82 | 108 | DHE, HEC |
| 3 | 86 | 0.69 | 0.93 | 26 | empty |
| 4 | 460 | 0.66 | 0.79 | 38 | empty |
| 5 | 184 | 0.52 | 0.78 | 29 | BU3 |
Interfaces
1 interface between chains.
- A–B · 674 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme c attachment).
Compared structures
- 6RTD · 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 6RTD · PDBe 6RTD · UniProt A0A0C7D2F2
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