Research workbench
Crystal structure of the vitamin B12 biosynthetic cobaltochelatase, cbixs, from archaeoglobus fulgidus
Analyse Crystal structure of the vitamin B12 biosynthetic cobaltochelatase, cbixs, from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DJ5
- Type
- protein
- Length
- 251 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sirohydrochlorin cobaltochelatase
- EC
- 4.99.1.3
- UniProt
- O29537
- Ligands
- PO4
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sirohydrochlorin cobaltochelatase (EC 4.99.1.3) | protein | 126 | 35% helix, 23% strand | O29537 |
| B | Sirohydrochlorin cobaltochelatase (EC 4.99.1.3) | protein | 125 | 38% helix, 23% strand | O29537 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 361 | 0.67 | 0.81 | 28 | GOL, PO4 |
| 2 | 83 | 0.42 | 0.80 | 18 | empty |
| 3 | 90 | 0.41 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2087 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 2DJ5 · Crystal Structure of the vitamin B12 biosynthetic cobaltochelatase, CbiXS, from… · the same entry in another collection · chain B against B, TM-score 1.00
- O29537 · AlphaFold monomer V2.0 prediction for sirohydrochlorin cobaltochelatase (O29537) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 O29537
- Elsewhere: RCSB PDB 2DJ5 · PDBe 2DJ5 · UniProt O29537
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