MolNFT v1 · #5443 · protein
Crystal structure of phosphonoacetate hydrolase complexed with phosphonoformate
1EI6: “Crystal structure of phosphonoacetate hydrolase complexed with phosphonoformate”. X-ray diffraction, 2 ligands (PPF, ZN), 16 pockets (best druggability 0.81). MolNFT v1 #5443 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1EI6
- Type
- protein
- Length
- 1,603 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphonoacetate hydrolase
- EC
- 3.11.1.2
- UniProt
- Q51782
- Ligands
- PPF, ZN
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphonoacetate hydrolase (EC 3.11.1.2) | protein | 404 | 36% helix, 23% strand | Q51782 |
| B | Phosphonoacetate hydrolase (EC 3.11.1.2) | protein | 403 | 36% helix, 22% strand | Q51782 |
| C | Phosphonoacetate hydrolase (EC 3.11.1.2) | protein | 401 | 34% helix, 23% strand | Q51782 |
| D | Phosphonoacetate hydrolase (EC 3.11.1.2) | protein | 395 | 36% helix, 21% strand | Q51782 |
Ligands and binding sites
- PPF · Phosphonoformic acid · ligand · 3 copies · chains A, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- TLA · L(+)-tartaric acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.81 | 0.97 | 23 | empty |
| 2 | 1089 | 0.81 | 0.82 | 69 | PPF |
| 3 | 156 | 0.80 | 0.96 | 26 | empty |
| 4 | 495 | 0.75 | 0.83 | 38 | PPF |
| 5 | 615 | 0.73 | 0.80 | 65 | TLA |
Interfaces
3 interfaces between chains.
- A–D · 1282 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1275 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 529 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1EI6 · Crystal structure of phosphonoacetate hydrolase complexed with phosphonoformate · the same entry in another collection · chain D against D, TM-score 1.00
- Q51782 · AlphaFold monomer V2.0 prediction for phosphonoacetate hydrolase (Q51782) · a predicted model of the same protein · chain C 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
- Every structure of UniProt Q51782
- Elsewhere: RCSB PDB 1EI6 · PDBe 1EI6 · UniProt Q51782
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