MolNFT v1 · #172656 · protein
Crystal structure of rubredoxin B (RV3250C) from mycobacterium tuberculosis
7A9A: “Crystal structure of rubredoxin B (RV3250C) from mycobacterium tuberculosis”. X-ray diffraction, 3 ligands (ZN, FE, CL), 3 pockets (best druggability 0.36). MolNFT v1 #172656 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7A9A
- Type
- protein
- Length
- 471 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rubredoxin
- UniProt
- I6YFL7
- Ligands
- ZN, FE, CL
- Pockets
- 3 · best druggability 0.36
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, F, G | Rubredoxin | protein | 60 | 15% helix, 25% strand | I6YFL7 |
| B, E, H | Rubredoxin | protein | 57 | 16% helix, 25% strand | I6YFL7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 40 copies · chains A, B, H, C, D, E, F, G
- FE · Fe (III) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · chains B, C
- GOL · Glycerol · additive · 4 copies · chains C, F, E, H
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains D, E, G, H
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, E, B, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.36 | 0.75 | 26 | empty |
| 2 | 89 | 0.36 | 0.76 | 22 | GOL |
| 3 | 69 | 0.32 | 0.75 | 15 | empty |
Interfaces
10 interfaces between chains.
- E–F · 199 Ų buried · 3 hydrogen bonds · protein-protein
- B–H · 194 Ų buried · 3 hydrogen bonds · protein-protein
- F–G · 190 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 176 Ų buried · 3 hydrogen bonds · protein-protein
- D–H · 171 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7A9A · Crystal structure of rubredoxin B (Rv3250c) from Mycobacterium tuberculosis · 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 I6YFL7
- Elsewhere: RCSB PDB 7A9A · PDBe 7A9A · UniProt I6YFL7
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