MolNFT v1 · #175911 · protein
Structure of mycobacterium smegmatis bd complex in the apo-form.
7D5I · Cytochrome D ubiquinol oxidase subunit 1: “Structure of mycobacterium smegmatis bd complex in the apo-form.”. Electron microscopy, 2 ligands (HEB, HDD), 11 pockets (best druggability 0.86). MolNFT v1 #175911 on GenesisL1: 3D…
- PDB
- 7D5I
- Type
- protein
- Length
- 793 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome D ubiquinol oxidase subunit 1; Integral membrane cytochrome D ubiquinol…
- EC
- 1.10.3.-, 3.1.3.1
- UniProt
- A0QXA8, I7GAS8
- Ligands
- HEB, HDD
- Pockets
- 11 · best druggability 0.86
Structure
electron microscopy · 2 distinct chains · 72% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome D ubiquinol oxidase subunit 1 (EC 1.10.3.-) | protein | 443 | 71% helix, 2% strand | A0QXA8 |
| B | Integral membrane cytochrome D ubiquinol oxidase (subunit II) cydb (EC 3.1.3.1) | protein | 350 | 72% helix, 2% strand | I7GAS8 |
Ligands and binding sites
- HEB · Heme B/C · ligand · 2 copies · chains A
- HDD · Cis-heme D hydroxychlorin gamma-spirolactone · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 810 | 0.86 | 0.89 | 60 | HEB, HDD |
| 2 | 354 | 0.76 | 0.86 | 42 | HEB |
| 3 | 102 | 0.75 | 0.95 | 30 | empty |
| 4 | 406 | 0.73 | 0.83 | 50 | empty |
| 5 | 221 | 0.68 | 0.85 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 3626 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 7D5I · Structure of Mycobacterium smegmatis bd complex in the apo-form. · 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 A0QXA8
- Every structure of UniProt I7GAS8
- Elsewhere: RCSB PDB 7D5I · PDBe 7D5I · UniProt A0QXA8 · UniProt I7GAS8
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