MolNFT v1 · #48525 · protein
Crystal structure of trans-aconitate bound to methylaconitate isomerase prpf from shewanella oneidensis
2PW0 · Prpf methylaconitate isomerase: “Crystal structure of trans-aconitate bound to methylaconitate isomerase prpf from shewanella oneidensis”. X-ray diffraction, 1 ligand (TRC), 7 pockets (best druggability 0.66). MolNFT v1 #48525 on…
- PDB
- 2PW0
- Type
- protein
- Length
- 726 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prpf methylaconitate isomerase
- UniProt
- Q8EJW4
- Ligands
- TRC
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prpf methylaconitate isomerase | protein | 385 | 21% helix, 37% strand | Q8EJW4 |
| B | Prpf methylaconitate isomerase | protein | 341 | 16% helix, 38% strand | Q8EJW4 |
Ligands and binding sites
- TRC · Tricarballylic acid · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 627 | 0.66 | 0.76 | 65 | empty |
| 2 | 194 | 0.52 | 0.78 | 36 | TRC |
| 3 | 79 | 0.47 | 0.82 | 24 | EDO |
| 4 | 53 | 0.45 | 0.84 | 20 | EDO |
| 5 | 74 | 0.32 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 288 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2PW0 · crystal structure of trans-aconitate bound to methylaconitate isomerase PrpF from… · the same entry in another collection · chain B against B, 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 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 Q8EJW4
- Elsewhere: RCSB PDB 2PW0 · PDBe 2PW0 · UniProt Q8EJW4
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