Research workbench
Crystal structure of cobt complexed with N1-(5'-phosphoribosyl)- benzimidazole and nicotinate
Analyse Crystal structure of cobt complexed with N1-(5'-phosphoribosyl)- benzimidazole… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1L5K
- Type
- protein
- Length
- 346 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
- EC
- 2.4.2.21
- UniProt
- Q05603
- Ligands
- 1RB, NIO
- Pockets
- 1 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase (EC 2.4.2.21) | protein | 346 | 52% helix, 11% strand | Q05603 |
Ligands and binding sites
- 1RB · 1-alpha-D-ribofuranosyl-benzimiazole-5'-phosphate · ligand · chains A
- NIO · Nicotinic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.66 | 0.86 | 33 | 1RB, NIO |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1L5K · Crystal Structure of CobT complexed with N1-(5'-phosphoribosyl)-benzimidazole and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q05603 · AlphaFold monomer V2.0 prediction for nicotinate-nucleotide-- dimethylbenzimidazole… · a predicted model of the same protein · 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 Q05603
- Elsewhere: RCSB PDB 1L5K · PDBe 1L5K · UniProt Q05603
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