MolNFT v1 · #29031 · protein
Crystal structure of the succinylglutamate desuccinylase from chromobacterium violaceum, northeast structural genomics target CVR22.
1YW4: “Crystal structure of the succinylglutamate desuccinylase from chromobacterium violaceum, northeast structural…”. X-ray diffraction, 1 ligand (ZN), 8 pockets (best druggability 0.79). MolNFT v1 #29031 on GenesisL1: 3D structure…
- PDB
- 1YW4
- Type
- protein
- Length
- 628 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinylglutamate desuccinylase
- EC
- 3.1.-.-
- UniProt
- Q7NU26
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinylglutamate desuccinylase (EC 3.1.-.-) | protein | 319 | 26% helix, 24% strand | Q7NU26 |
| B | Succinylglutamate desuccinylase (EC 3.1.-.-) | protein | 309 | 30% helix, 23% strand | Q7NU26 |
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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 997 | 0.79 | 0.81 | 77 | empty |
| 2 | 498 | 0.65 | 0.77 | 46 | ZN |
| 3 | 101 | 0.53 | 0.83 | 18 | empty |
| 4 | 50 | 0.43 | 0.84 | 16 | empty |
| 5 | 74 | 0.40 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 365 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 1YW4 · Crystal Structure of the Succinylglutamate Desuccinylase from Chromobacterium violaceum… · the same entry in another collection · chain A against A, TM-score 1.00
- Q7NU26 · AlphaFold monomer V2.0 prediction for succinylglutamate desuccinylase (Q7NU26) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q7NU26
- Elsewhere: RCSB PDB 1YW4 · PDBe 1YW4 · UniProt Q7NU26
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