MolNFT v1 · #48524 · protein
Crystal structure of methylaconitate isomerase prpf from shewanella oneidensis
2PVZ · Prpf methylaconitate isomerase: “Crystal structure of methylaconitate isomerase prpf from shewanella oneidensis”. X-ray diffraction, 1 ligand (CA), 8 pockets (best druggability 0.75). MolNFT v1 #48524 on GenesisL1: 3D structure…
- PDB
- 2PVZ
- Type
- protein
- Length
- 774 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prpf methylaconitate isomerase
- UniProt
- Q8EJW4
- Ligands
- CA
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Prpf methylaconitate isomerase | protein | 387 | 22% helix, 36% strand | Q8EJW4 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.75 | 0.78 | 97 | CA, EDO |
| 2 | 55 | 0.47 | 0.85 | 23 | EDO |
| 3 | 94 | 0.47 | 0.80 | 24 | empty |
| 4 | 66 | 0.40 | 0.80 | 20 | empty |
| 5 | 94 | 0.39 | 0.77 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 2517 Ų buried · 57 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 2PVZ · Crystal structure of methylaconitate isomerase PrpF from Shewanella oneidensis · the same entry in another collection · chain A against A, TM-score 1.00
- Q8EJW4 · AlphaFold monomer V2.0 prediction for 2-methyl-aconitate isomerase (Q8EJW4) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8EJW4
- Elsewhere: RCSB PDB 2PVZ · PDBe 2PVZ · UniProt Q8EJW4
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