Research workbench
Crystal structure of putative thioesterase yhda from lactococcus lactis. northeast structural genomics consortium target KR113
Analyse Crystal structure of putative thioesterase yhda from lactococcus lactis.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
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