MolNFT v1 · #90079 · protein
Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans PD1222 (target nysgrc-012907) with bound mg
4E8G · Mandelate RACEMASE/MUCONATE lactonizing enzyme, N-terminal…: “Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans PD1222 (target…”. X-ray diffraction, 2 ligands (UNL, MG), 7 pockets (best…
- PDB
- 4E8G
- Type
- protein
- Length
- 721 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
- UNL, MG
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mandelate RACEMASE/MUCONATE lactonizing enzyme, N-terminal domain protein | protein | 354 | 40% helix, 20% strand | A1B198 |
| B | Mandelate RACEMASE/MUCONATE lactonizing enzyme, N-terminal domain protein | protein | 367 | 39% helix, 22% strand | A1B198 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.80 | 0.97 | 28 | empty |
| 2 | 145 | 0.55 | 0.82 | 29 | empty |
| 3 | 136 | 0.55 | 0.82 | 27 | empty |
| 4 | 106 | 0.51 | 0.81 | 21 | empty |
| 5 | 117 | 0.43 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1328 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 4E8G · Crystal structure of an enolase (mandelate racemase subgroup) from paracococus… · the same entry in another collection · chain A against A, 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 4E8G · PDBe 4E8G · UniProt A1B198
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