MolNFT v1 · #149822 · protein
Repertoires of functionally diverse enzymes through computational design at epistatic active-site positions
6GBK · Parathion hydrolase: “Repertoires of functionally diverse enzymes through computational design at epistatic active-site positions”. X-ray diffraction, 1 ligand (ZN), 8 pockets (best druggability 0.66). MolNFT v1 #149822 on…
- PDB
- 6GBK
- Type
- protein
- Length
- 656 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
- 8 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Parathion hydrolase (EC 3.1.8.1) | protein | 327 | 52% helix, 14% strand | P0A434 |
| B | Parathion hydrolase (EC 3.1.8.1) | protein | 329 | 51% 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
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.66 | 0.88 | 31 | empty |
| 2 | 260 | 0.65 | 0.82 | 34 | FMT, ZN, TRS |
| 3 | 253 | 0.62 | 0.81 | 35 | FMT |
| 4 | 74 | 0.36 | 0.77 | 16 | empty |
| 5 | 55 | 0.34 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1425 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 6GBK · 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 6GBK · PDBe 6GBK · UniProt P0A434
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