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Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans PD1222 (target nysgrc-012907) with bound cis-4OH-D-proline betaine (product)
Analyse Crystal structure of an enolase (mandelate racemase subgroup) from paracococus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IZG
- 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
- 4OP, MG, IOD
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mandelate RACEMASE/MUCONATE lactonizing enzyme, N-terminal domain protein | protein | 369 | 38% helix, 22% strand | A1B198 |
Ligands and binding sites
- 4OP · (2S,4S)-2-carboxy-4-hydroxy-1,1-dimethylpyrrolidinium · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 5 copies · chains A, B
- IOD · Iodide ion · ion · 27 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.82 | 0.97 | 32 | empty |
| 2 | 51 | 0.71 | 0.99 | 18 | 4OP |
| 3 | 132 | 0.55 | 0.82 | 25 | IOD |
| 4 | 141 | 0.55 | 0.82 | 27 | IOD |
| 5 | 111 | 0.41 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1328 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 4IZG · 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 4IZG · PDBe 4IZG · UniProt A1B198
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