Research workbench
1.5 ångström crystal structure of a novel cobalamin-binding protein from desulfitobacterium hafniense dcb-2
Analyse 1.5 ångström crystal structure of a novel cobalamin-binding protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JGI
- Type
- protein
- Length
- 411 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein
- UniProt
- Q8RPG0
- Ligands
- COB
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein | protein | 205 | 60% helix, 12% strand | Q8RPG0 |
| B | Putative uncharacterized protein | protein | 206 | 61% helix, 12% strand | Q8RPG0 |
Ligands and binding sites
- COB · Co-methylcobalamin · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.63 | 0.85 | 29 | empty |
| 2 | 195 | 0.61 | 0.82 | 28 | empty |
| 3 | 130 | 0.47 | 0.78 | 19 | empty |
| 4 | 54 | 0.26 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 362 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4JGI · 1.5 Angstrom crystal structure of a novel cobalamin-binding protein 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 Q8RPG0
- Elsewhere: RCSB PDB 4JGI · PDBe 4JGI · UniProt Q8RPG0
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