MolNFT v1 · #47891 · protein
Crystal structure of putative mandelate RACEMASE/MUCONATE lactonizing enzyme from roseovarius nubinhibens ism
2PCE: “Crystal structure of putative mandelate RACEMASE/MUCONATE lactonizing enzyme from roseovarius nubinhibens ism”. X-ray diffraction, 1 ligand (PO4), 20 pockets (best druggability 0.84). MolNFT v1 #47891 on GenesisL1: 3D structure…
- PDB
- 2PCE
- Type
- protein
- Length
- 2,973 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative mandelate RACEMASE/MUCONATE lactonizing enzyme
- UniProt
- A3SNG0
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, G, H | Putative mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 372 | 36% helix, 23% strand | A3SNG0 |
| B | Putative mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 371 | 37% helix, 23% strand | A3SNG0 |
| F | Putative mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 370 | 37% helix, 23% strand | A3SNG0 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.84 | 0.92 | 64 | empty |
| 2 | 373 | 0.84 | 0.92 | 60 | PO4 |
| 3 | 353 | 0.83 | 0.93 | 64 | empty |
| 4 | 309 | 0.83 | 0.93 | 52 | empty |
| 5 | 1026 | 0.77 | 0.79 | 63 | empty |
Interfaces
16 interfaces between chains.
- A–D · 1131 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1127 Ų buried · 12 hydrogen bonds · protein-protein
- B–G · 1125 Ų buried · 11 hydrogen bonds · protein-protein
- C–H · 1098 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 1073 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2PCE · Crystal structure of putative mandelate racemase/muconate lactonizing enzyme from… · the same entry in another collection · chain H against H, 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 A3SNG0
- Elsewhere: RCSB PDB 2PCE · PDBe 2PCE · UniProt A3SNG0
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