MolNFT v1 · #114283 · protein
Crystal structure of hyperthermophilic thermotoga maritima L-ketose-3- epimerase with CO2+
5B7Y · Uncharacterized protein TM_0416: “Crystal structure of hyperthermophilic thermotoga maritima L-ketose-3- epimerase with CO2+”. X-ray diffraction, 2 ligands (1PG, CO), 3 pockets (best druggability 0.76). MolNFT v1 #114283 on…
- PDB
- 5B7Y
- Type
- protein
- Length
- 537 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein TM_0416
- UniProt
- Q9WYP7
- Ligands
- 1PG, CO
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein TM_0416 | protein | 269 | 50% helix, 14% strand | Q9WYP7 |
| B | Uncharacterized protein TM_0416 | protein | 268 | 50% helix, 14% strand | Q9WYP7 |
Ligands and binding sites
- 1PG · 2-(2-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol · ligand · 3 copies · chains A, B
- CO · Cobalt (II) ion · metal · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 847 | 0.76 | 0.79 | 77 | 1PG, MPD |
| 2 | 300 | 0.62 | 0.80 | 34 | MPD |
| 3 | 298 | 0.61 | 0.79 | 32 | MPD |
Interfaces
1 interface between chains.
- A–B · 548 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5B7Y · Crystal Structure of Hyperthermophilic Thermotoga maritima L-Ketose-3-Epimerase with Co2+ · the same entry in another collection · chain A against A, TM-score 1.00
- Q9WYP7 · AlphaFold monomer V2.0 prediction for 5-keto-L-gluconate epimerase (Q9WYP7) · a predicted model of the same protein · chain A 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 Q9WYP7
- Elsewhere: RCSB PDB 5B7Y · PDBe 5B7Y · UniProt Q9WYP7
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