MolNFT v1 · #100037 · protein
Crystal structure of phnz from uncultured bacterium HF130_AEPN_1
4MLM · Predicted hd phosphohydrolase phnz: “Crystal structure of phnz from uncultured bacterium HF130_AEPN_1”. X-ray diffraction, 3 ligands (FE, NA, SO4), 4 pockets (best druggability 0.75). MolNFT v1 #100037 on GenesisL1: 3D structure…
- PDB
- 4MLM
- Type
- protein
- Length
- 375 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Predicted hd phosphohydrolase phnz
- UniProt
- D0E8I5
- Ligands
- FE, NA, SO4
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Predicted hd phosphohydrolase phnz | protein | 188 | 69% helix, 3% strand | D0E8I5 |
| B | Predicted hd phosphohydrolase phnz | protein | 187 | 67% helix, 3% strand | D0E8I5 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · chains B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
- BOG · octyl beta-D-glucopyranoside · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 736 | 0.75 | 0.80 | 61 | GOL, BOG, FE, TLA |
| 2 | 97 | 0.42 | 0.78 | 23 | FE, TLA |
| 3 | 56 | 0.30 | 0.75 | 20 | SO4 |
| 4 | 51 | 0.23 | 0.72 | 9 | empty |
Interfaces
1 interface between chains.
- A–B · 654 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 4MLM · Crystal Structure of PhnZ from uncultured bacterium HF130_AEPn_1 · the same entry in another collection · chain A against A, TM-score 1.00
- D0E8I5 · AlphaFold monomer V2.0 prediction for 2-amino-1-hydroxyethylphosphonate dioxygenase… · a predicted model of the same protein · chain B against A, TM-score 0.91
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 D0E8I5
- Elsewhere: RCSB PDB 4MLM · PDBe 4MLM · UniProt D0E8I5
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