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Crystal structure of a tartrate dehydratase from azospirillum, target efi-502395, with bound mg and a putative acrylate ion, ordered active site
Analyse Crystal structure of a tartrate dehydratase from azospirillum, target… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KEM
- Type
- protein
- Length
- 780 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing enzyme
- UniProt
- D3P639
- Ligands
- AKR, MG, CL
- Pockets
- 9 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 390 | 41% helix, 18% strand | D3P639 |
Ligands and binding sites
- AKR · Acrylic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.49 | 0.78 | 26 | empty |
| 2 | 160 | 0.48 | 0.77 | 26 | empty |
| 3 | 141 | 0.45 | 0.76 | 21 | empty |
| 4 | 130 | 0.43 | 0.76 | 21 | empty |
| 5 | 124 | 0.42 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1882 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 4KEM · Crystal structure of a tartrate dehydratase from azospirillum, target efi-502395, with… · the same entry in another collection · 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 D3P639
- Elsewhere: RCSB PDB 4KEM · PDBe 4KEM · UniProt D3P639
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