MolNFT v1 · #121010 · protein
Crystal structure of a reconstructed lactonase ancestor, ANC1-mph, of the bacterial methyl parathion hydrolase, mph.
5HIF: “Crystal structure of a reconstructed lactonase ancestor, ANC1-mph, of the bacterial methyl parathion…”. X-ray diffraction, 2 ligands (ZN, MG), 5 pockets (best druggability 0.85). MolNFT v1 #121010 on GenesisL1: 3D structure, binding…
- PDB
- 5HIF
- Type
- protein
- Length
- 598 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reconstructed lactonase ancestor, ANC1-mph
- EC
- 3.1.1.35
- Ligands
- ZN, MG
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Reconstructed lactonase ancestor, ANC1-mph (EC 3.1.1.35) | protein | 299 | 28% helix, 29% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1176 | 0.85 | 0.86 | 113 | empty |
| 2 | 57 | 0.62 | 0.92 | 16 | PEG |
| 3 | 136 | 0.57 | 0.82 | 26 | PEG |
| 4 | 53 | 0.35 | 0.78 | 16 | empty |
| 5 | 60 | 0.30 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2356 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 5HIF · Crystal structure of a reconstructed lactonase ancestor, Anc1-MPH, of the bacterial… · 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 5HIF · PDBe 5HIF
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