MolNFT v1 · #52705 · protein
Crystal structure of a catalytically promiscuous phosphonate monoester hydrolase from burkholderia caryophylli
2W8S: “Crystal structure of a catalytically promiscuous phosphonate monoester hydrolase from burkholderia caryophylli”. X-ray diffraction, 3 ligands (ZN, FE, SO4), 20 pockets (best druggability 0.83). MolNFT v1 #52705 on GenesisL1: 3D…
- PDB
- 2W8S
- Type
- protein
- Length
- 2,051 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphonate monoester hydrolase
- UniProt
- Q45087
- Ligands
- ZN, FE, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphonate monoester hydrolase | protein | 512 | 35% helix, 16% strand | Q45087 |
| B, C, D | Phosphonate monoester hydrolase | protein | 513 | 36% helix, 16% strand | Q45087 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1161 | 0.83 | 0.84 | 120 | empty |
| 2 | 1084 | 0.83 | 0.84 | 107 | GOL |
| 3 | 211 | 0.76 | 0.91 | 37 | empty |
| 4 | 708 | 0.75 | 0.80 | 61 | empty |
| 5 | 647 | 0.75 | 0.81 | 54 | empty |
Interfaces
4 interfaces between chains.
- C–D · 3004 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 2911 Ų buried · 43 hydrogen bonds · protein-protein
- B–D · 1570 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1545 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 2W8S · CRYSTAL STRUCTURE OF A catalytically promiscuous PHOSPHONATE MONOESTER HYDROLASE FROM… · the same entry in another collection · chain D against D, TM-score 1.00
- Q45087 · AlphaFold monomer V2.0 prediction for multifunctional alkaline phosphatase superfamily… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q45087
- Elsewhere: RCSB PDB 2W8S · PDBe 2W8S · UniProt Q45087
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