MolNFT v1 · #31928 · protein
Crystal structure of cobalamin biosynthesis precorrin-6Y methylase (cbie) from archaeoglobus fulgidus
2BB3: “Crystal structure of cobalamin biosynthesis precorrin-6Y methylase (cbie) from archaeoglobus fulgidus”. X-ray diffraction, 1 ligand (SAH), 4 pockets (best druggability 0.73). MolNFT v1 #31928 on GenesisL1: 3D structure, binding…
- PDB
- 2BB3
- Type
- protein
- Length
- 387 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cobalamin biosynthesis precorrin-6Y methylase (cbie)
- EC
- 2.1.1.-
- UniProt
- O29536
- Ligands
- SAH
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cobalamin biosynthesis precorrin-6Y methylase (cbie) (EC 2.1.1.-) | protein | 194 | 29% helix, 27% strand | O29536 |
| B | Cobalamin biosynthesis precorrin-6Y methylase (cbie) (EC 2.1.1.-) | protein | 193 | 28% helix, 27% strand | O29536 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 763 | 0.73 | 0.79 | 65 | SAH |
| 2 | 200 | 0.47 | 0.75 | 28 | empty |
| 3 | 54 | 0.40 | 0.81 | 12 | empty |
| 4 | 60 | 0.33 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 548 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified, 2 disulfide (engineered, disulfide, nonstandard).
Compared structures
- 2BB3 · Crystal Structure of Cobalamin Biosynthesis Precorrin-6Y Methylase (cbiE) from… · 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 O29536
- Elsewhere: RCSB PDB 2BB3 · PDBe 2BB3 · UniProt O29536
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