MolNFT v1 · #64817 · protein
Crystal structure of putative thioesterase yhda from lactococcus lactis. northeast structural genomics consortium target KR113
3GEK: “Crystal structure of putative thioesterase yhda from lactococcus lactis. northeast structural genomics…”. X-ray diffraction, 8 pockets (best druggability 0.70). MolNFT v1 #64817 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3GEK
- Type
- protein
- Length
- 507 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative thioesterase yhda
- UniProt
- Q9CHK5
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative thioesterase yhda | protein | 132 | 23% helix, 48% strand | Q9CHK5 |
| B | Putative thioesterase yhda | protein | 125 | 22% helix, 52% strand | Q9CHK5 |
| C | Putative thioesterase yhda | protein | 127 | 20% helix, 53% strand | Q9CHK5 |
| D | Putative thioesterase yhda | protein | 123 | 22% helix, 50% strand | Q9CHK5 |
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.70 | 0.84 | 37 | empty |
| 2 | 96 | 0.64 | 0.89 | 23 | empty |
| 3 | 128 | 0.62 | 0.86 | 26 | empty |
| 4 | 74 | 0.58 | 0.88 | 16 | empty |
| 5 | 166 | 0.50 | 0.78 | 26 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1309 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1283 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 566 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 560 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 228 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3GEK · Crystal structure of putative thioesterase yhdA from Lactococcus lactis. Northeast… · the same entry in another collection · 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 Q9CHK5
- Elsewhere: RCSB PDB 3GEK · PDBe 3GEK · UniProt Q9CHK5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.