Research workbench
Repertoires of functionally diverse enzymes through computational design at epistatic active-site positions
Analyse Repertoires of functionally diverse enzymes through computational design at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GBL
- Type
- protein
- Length
- 655 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Parathion hydrolase
- EC
- 3.1.8.1
- UniProt
- P0A434
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Parathion hydrolase (EC 3.1.8.1) | protein | 328 | 51% helix, 14% strand | P0A434 |
| B | Parathion hydrolase (EC 3.1.8.1) | protein | 327 | 52% helix, 14% strand | P0A434 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- CAC · Cacodylate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.70 | 0.94 | 27 | empty |
| 2 | 201 | 0.61 | 0.82 | 35 | FMT, ZN, CAC, EDO |
| 3 | 228 | 0.60 | 0.81 | 35 | ZN, EDO, CAC |
| 4 | 81 | 0.40 | 0.78 | 19 | empty |
| 5 | 81 | 0.38 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1484 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 6GBL · Repertoires of functionally diverse enzymes through computational design at epistatic… · the same entry in another collection · chain B against B, 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 P0A434
- Elsewhere: RCSB PDB 6GBL · PDBe 6GBL · UniProt P0A434
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