Research workbench
Crystal structure of a glucarate dehydratase related protein, from actinobacillus succinogenes, target efi-502312, with sodium and sulfate bound, ordered loop
Analyse Crystal structure of a 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
- 4G8T
- Type
- protein
- Length
- 1,764 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucarate dehydratase
- EC
- 4.2.1.40
- UniProt
- A6VQF1
- Ligands
- NA, SO4
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glucarate dehydratase (EC 4.2.1.40) | protein | 441 | 38% helix, 17% strand | A6VQF1 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 7 copies · chains A, D, B, C
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 3 copies · chains B, C, D
- DTU · (2R,3S)-1,4-dimercaptobutane-2,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.84 | 0.85 | 141 | GOL |
| 2 | 1057 | 0.81 | 0.83 | 118 | GOL |
| 3 | 446 | 0.71 | 0.82 | 57 | GOL |
| 4 | 197 | 0.69 | 0.87 | 28 | empty |
| 5 | 199 | 0.69 | 0.86 | 34 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1355 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1327 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 712 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 691 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 414 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (additive adduct).
Compared structures
- 4G8T · Crystal structure of a 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 A6VQF1
- Elsewhere: RCSB PDB 4G8T · PDBe 4G8T · UniProt A6VQF1
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