MolNFT v1 · #13251 · protein
Crystal structure of cobt complexed with 3,4-dimethylphenol and nicotinate mononucleotide
1L5O · Nicotinate-nucleotide--dimethylbenzimidazole…: “Crystal structure of cobt complexed with 3,4-dimethylphenol and nicotinate mononucleotide”. X-ray diffraction, 2 ligands (2MP, NCN), 1 pocket (best druggability 0.67). MolNFT v1 #13251…
- PDB
- 1L5O
- 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
- 2MP, NCN
- Pockets
- 1 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase (EC 2.4.2.21) | protein | 346 | 51% helix, 11% strand | Q05603 |
Ligands and binding sites
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 | 166 | 0.67 | 0.87 | 32 | 2MP, NCN |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1L5O · Crystal Structure of CobT complexed with 3,4-dimethylphenol and nicotinate mononucleotide · 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 1L5O · PDBe 1L5O · UniProt Q05603
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