MolNFT v1 · #114284 · protein
Crystal structure of hyperthermophilic thermotoga maritima L-ketose-3- epimerase with NI2+
5B7Z · Uncharacterized protein TM_0416: “Crystal structure of hyperthermophilic thermotoga maritima L-ketose-3- epimerase with NI2+”. X-ray diffraction, 2 ligands (1PG, NI), 4 pockets (best druggability 0.75). MolNFT v1 #114284 on…
- PDB
- 5B7Z
- 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, NI
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 51% 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 | 51% helix, 14% strand | Q9WYP7 |
Ligands and binding sites
- 1PG · 2-(2-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol · ligand · 4 copies · chains A, B
- NI · Nickel (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
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 | 798 | 0.75 | 0.80 | 64 | MPD, 1PG |
| 2 | 315 | 0.64 | 0.80 | 38 | MPD |
| 3 | 323 | 0.62 | 0.79 | 32 | MPD |
| 4 | 90 | 0.34 | 0.74 | 28 | 1PG |
Interfaces
1 interface between chains.
- A–B · 547 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5B7Z · Crystal Structure of Hyperthermophilic Thermotoga maritima L-Ketose-3-Epimerase with Ni2+ · 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 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 Q9WYP7
- Elsewhere: RCSB PDB 5B7Z · PDBe 5B7Z · UniProt Q9WYP7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.