Research workbench
Crystal structure of D-glucarate dehydratase related protein from actinobacillus succinogenes complexed with D-glucarate
Analyse Crystal structure of D-glucarate dehydratase related protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PFR
- Type
- protein
- Length
- 1,704 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing protein
- UniProt
- A6VQF6
- Ligands
- GKR, MG
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 426 | 39% helix, 18% strand | A6VQF6 |
Ligands and binding sites
- GKR · D-glucarate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1165 | 0.83 | 0.84 | 139 | empty |
| 2 | 771 | 0.82 | 0.85 | 82 | empty |
| 3 | 629 | 0.70 | 0.78 | 66 | GKR |
| 4 | 625 | 0.70 | 0.78 | 74 | GKR |
| 5 | 599 | 0.69 | 0.78 | 64 | GKR |
Interfaces
6 interfaces between chains.
- A–D · 1372 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1370 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 770 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 766 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 394 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 56 modified (engineered).
Compared structures
- 3PFR · Crystal structure of D-Glucarate dehydratase related protein from Actinobacillus… · 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 A6VQF6
- Elsewhere: RCSB PDB 3PFR · PDBe 3PFR · UniProt A6VQF6
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