MolNFT v1 · #54665 · protein
Cobalt chelatase cbik (periplasmatic) from desulvobrio vulgaris hildenborough (co-crystallized with cobalt)
2XVZ · Chelatase, putative: “Cobalt chelatase cbik (periplasmatic) from desulvobrio vulgaris hildenborough (co-crystallized with cobalt)”. X-ray diffraction, 6 ligands (HEM, CO, NA), 1 pocket (best druggability 0.69). MolNFT v1 #54665 on…
- PDB
- 2XVZ
- Type
- protein
- Length
- 263 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chelatase, putative
- EC
- 4.99.1.3
- UniProt
- Q72EC8
- Ligands
- HEM, CO, NA, SO4, CL, PER
- Pockets
- 1 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chelatase, putative (EC 4.99.1.3) | protein | 263 | 44% helix, 17% strand | Q72EC8 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- CO · Cobalt (II) ion · metal · chains A
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 8 copies · chains A
- CL · Chloride ion · ion · chains A
- PER · Peroxide ion · ion · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 266 | 0.69 | 0.84 | 37 | SO4, NA |
Compared structures
- 2XVZ · Cobalt chelatase CbiK (periplasmatic) from Desulvobrio vulgaris Hildenborough… · the same entry in another collection · chain A against A, TM-score 1.00
- Q72EC8 · AlphaFold monomer V2.0 prediction for sirohydrochlorin cobaltochelatase cbikp (Q72EC8) · a predicted model of the same protein · 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 Q72EC8
- Elsewhere: RCSB PDB 2XVZ · PDBe 2XVZ · UniProt Q72EC8
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