Research workbench
The crystal structure of putative precorrin isomerase cbic in cobalamin biosynthesis
Analyse The crystal structure of putative precorrin isomerase cbic in cobalamin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AFV
- Type
- protein
- Length
- 434 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cobalamin biosynthesis precorrin isomerase
- EC
- 5.4.1.2
- UniProt
- Q8EXP7
- Ligands
- CL
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cobalamin biosynthesis precorrin isomerase (EC 5.4.1.2) | protein | 217 | 54% helix, 9% strand | Q8EXP7 |
Ligands and binding sites
- CL · Chloride ion · ion · 8 copies · chains A, B
- P6G · Hexaethylene glycol · additive · chains A
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 782 | 0.80 | 0.83 | 59 | CL |
| 2 | 730 | 0.80 | 0.84 | 51 | CL |
Interfaces
1 interface between chains.
- A–B · 1438 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2AFV · The Crystal Structure of Putative Precorrin Isomerase CbiC in Cobalamin Biosynthesis · the same entry in another collection · chain A against A, TM-score 1.00
- Q8EXP7 · AlphaFold monomer V2.0 prediction for cobalt-precorrin-8 methylmutase (Q8EXP7) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q8EXP7
- Elsewhere: RCSB PDB 2AFV · PDBe 2AFV · UniProt Q8EXP7
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