MolNFT v1 · #48224 · protein
Crystal structure of a mandelate RACEMASE/MUCONATE lactonizing enzyme from roseovarius sp. HTCC2601
2PMQ: “Crystal structure of a mandelate RACEMASE/MUCONATE lactonizing enzyme from roseovarius sp. HTCC2601”. X-ray diffraction, 1 ligand (MG), 5 pockets (best druggability 0.79). MolNFT v1 #48224 on GenesisL1: 3D structure, binding sites…
- PDB
- 2PMQ
- Type
- protein
- Length
- 741 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing enzyme
- UniProt
- Q0FPQ4
- Ligands
- MG
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 367 | 38% helix, 20% strand | Q0FPQ4 |
| B | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 374 | 37% helix, 22% strand | Q0FPQ4 |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1034 | 0.79 | 0.80 | 85 | empty |
| 2 | 140 | 0.39 | 0.73 | 23 | empty |
| 3 | 78 | 0.38 | 0.77 | 17 | empty |
| 4 | 61 | 0.34 | 0.77 | 18 | empty |
| 5 | 63 | 0.29 | 0.74 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 856 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 2PMQ · Crystal structure of a mandelate racemase/muconate lactonizing enzyme from Roseovarius… · the same entry in another collection · chain A against A, TM-score 1.00
- Q0FPQ4 · AlphaFold monomer V2.0 prediction for 4-hydroxyproline betaine 2-epimerase (Q0FPQ4) · 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 Q0FPQ4
- Elsewhere: RCSB PDB 2PMQ · PDBe 2PMQ · UniProt Q0FPQ4
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