MolNFT v1 · #143634 · protein
Crystal structure of nicotinate mononucleotide-5,6- dimethylbenzimidazole phosphoribosyltransferase cobt from yersinia enterocolitica
6B5F · Nicotinate-nucleotide--dimethylbenzimidazole…: “Crystal structure of nicotinate mononucleotide-5,6- dimethylbenzimidazole phosphoribosyltransferase cobt from…”. X-ray diffraction, 2 ligands (SO4, CL), 4 pockets (best druggability…
- PDB
- 6B5F
- Type
- protein
- Length
- 680 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
- EC
- 2.4.2.21
- UniProt
- A1JTP8
- Ligands
- SO4, CL
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase (EC 2.4.2.21) | protein | 344 | 51% helix, 9% strand | A1JTP8 |
| B | Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase (EC 2.4.2.21) | protein | 336 | 53% helix, 10% strand | A1JTP8 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · chains 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 | 212 | 0.73 | 0.89 | 44 | SO4 |
| 2 | 255 | 0.68 | 0.84 | 38 | SO4 |
| 3 | 73 | 0.36 | 0.77 | 17 | empty |
| 4 | 70 | 0.32 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1693 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6B5F · Crystal structure of nicotinate mononucleotide-5,6-dimethylbenzimidazole… · the same entry in another collection · chain A against A, TM-score 1.00
- A1JTP8 · AlphaFold monomer V2.0 prediction for nicotinate-nucleotide-- dimethylbenzimidazole… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 A1JTP8
- Elsewhere: RCSB PDB 6B5F · PDBe 6B5F · UniProt A1JTP8
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