MolNFT v1 · #95813 · protein
Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans PD1222 (target nysgrc-012907) with bound L- proline betaine (substrate)
4J1O · Mandelate RACEMASE/MUCONATE lactonizing enzyme, N-terminal…: “Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans PD1222 (target…”. X-ray diffraction, 3 ligands (PBE, MG, IOD), 7 pockets…
- PDB
- 4J1O
- Type
- protein
- Length
- 738 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing enzyme, N-terminal domain protein
- UniProt
- A1B198
- Ligands
- PBE, MG, IOD
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mandelate RACEMASE/MUCONATE lactonizing enzyme, N-terminal domain protein | protein | 369 | 39% helix, 22% strand | A1B198 |
Ligands and binding sites
- PBE · 1,1-dimethyl-prolinium · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 5 copies · chains A, B
- IOD · Iodide ion · ion · 11 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.80 | 0.97 | 29 | empty |
| 2 | 138 | 0.56 | 0.82 | 29 | IOD |
| 3 | 109 | 0.54 | 0.83 | 23 | IOD |
| 4 | 112 | 0.41 | 0.77 | 19 | empty |
| 5 | 108 | 0.40 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1326 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 4J1O · Crystal structure of an enolase (mandelate racemase subgroup) from paracococus… · the same entry in another collection · chain B against B, TM-score 1.00
- A1B198 · AlphaFold monomer V2.0 prediction for 4-hydroxyproline betaine 2-epimerase (A1B198) · 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 A1B198
- Elsewhere: RCSB PDB 4J1O · PDBe 4J1O · UniProt A1B198
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.