MolNFT v1 · #63261 · protein
Crystal structure of organophosphorus hydrolase from geobacillus stearothermophilus strain 10
3F4D: “Crystal structure of organophosphorus hydrolase from geobacillus stearothermophilus strain 10”. X-ray diffraction, 1 ligand (CO), 4 pockets (best druggability 0.74). MolNFT v1 #63261 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3F4D
- Type
- protein
- Length
- 648 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Organophosphorus hydrolase
- Ligands
- CO
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Organophosphorus hydrolase | protein | 324 | 48% helix, 15% strand | — |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 4 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1151 | 0.74 | 0.77 | 99 | empty |
| 2 | 511 | 0.70 | 0.79 | 63 | CO |
| 3 | 97 | 0.43 | 0.79 | 18 | empty |
| 4 | 81 | 0.42 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1669 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 3F4D · Crystal structure of organophosphorus hydrolase from Geobacillus stearothermophilus… · 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
- Elsewhere: RCSB PDB 3F4D · PDBe 3F4D
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