Research workbench
X-ray structure of succinylglutamate desuccinalase from vibrio parahaemolyticus (rimd 2210633) at the resolution 2.3 a, northeast structural genomics target VPR14
Analyse X-ray structure of succinylglutamate desuccinalase from vibrio parahaemolyticus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BCO
- Type
- protein
- Length
- 630 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinylglutamate desuccinylase
- EC
- 3.1.-.-
- UniProt
- Q87Q40
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinylglutamate desuccinylase (EC 3.1.-.-) | protein | 338 | 24% helix, 30% strand | Q87Q40 |
| B | Succinylglutamate desuccinylase (EC 3.1.-.-) | protein | 292 | 28% helix, 23% strand | Q87Q40 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 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 | 1023 | 0.79 | 0.80 | 61 | empty |
| 2 | 469 | 0.74 | 0.83 | 54 | ZN |
| 3 | 389 | 0.67 | 0.81 | 34 | empty |
| 4 | 304 | 0.67 | 0.82 | 39 | empty |
| 5 | 118 | 0.45 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 765 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 2BCO · X-ray structure of succinylglutamate desuccinalase from Vibrio Parahaemolyticus (RIMD… · the same entry in another collection · chain A against A, TM-score 1.00
- Q87Q40 · AlphaFold monomer V2.0 prediction for succinylglutamate desuccinylase (Q87Q40) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q87Q40
- Elsewhere: RCSB PDB 2BCO · PDBe 2BCO · UniProt Q87Q40
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