MolNFT v1 · #97825 · protein
Crystal structure of cobt S80Y/Q88M/L175M complexed with P-cresol
4KQK · Nicotinate-nucleotide--dimethylbenzimidazole…: “Crystal structure of cobt S80Y/Q88M/L175M complexed with P-cresol”. X-ray diffraction, 2 ligands (PCR, SO4), 4 pockets (best druggability 0.81). MolNFT v1 #97825 on GenesisL1: 3D…
- PDB
- 4KQK
- Type
- protein
- Length
- 691 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
- Q05603
- Ligands
- PCR, SO4
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase (EC 2.4.2.21) | protein | 347 | 52% helix, 11% strand | Q05603 |
| B | Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase (EC 2.4.2.21) | protein | 344 | 52% helix, 11% strand | Q05603 |
Ligands and binding sites
- PCR · P-cresol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.81 | 0.95 | 42 | SO4, PCR |
| 2 | 197 | 0.77 | 0.92 | 35 | SO4, PCR |
| 3 | 70 | 0.53 | 0.86 | 18 | empty |
| 4 | 65 | 0.33 | 0.76 | 18 | SO4 |
Interfaces
1 interface between chains.
- A–B · 2098 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4KQK · Crystal structure of CobT S80Y/Q88M/L175M complexed with p-cresol · 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 4KQK · PDBe 4KQK · UniProt Q05603
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