Research workbench
Crystal structure of a putative succinylglutamate desuccinylase / aspartoacylase family protein (SAMA_0604) from shewanella amazonensis SB2B at 1.80 a resolution
Analyse Crystal structure of a putative succinylglutamate desuccinylase /… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FMC
- Type
- protein
- Length
- 1,461 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative succinylglutamate desuccinylase / aspartoacylase
- UniProt
- A1S356
- Ligands
- SO4
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Putative succinylglutamate desuccinylase / aspartoacylase | protein | 365 | 30% helix, 30% strand | A1S356 |
| C | Putative succinylglutamate desuccinylase / aspartoacylase | protein | 366 | 31% helix, 29% strand | A1S356 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1107 | 0.80 | 0.82 | 117 | SO4 |
| 2 | 503 | 0.76 | 0.84 | 65 | SO4, GOL |
| 3 | 433 | 0.73 | 0.83 | 54 | SO4, GOL |
| 4 | 50 | 0.70 | 0.98 | 28 | empty |
| 5 | 51 | 0.66 | 0.96 | 18 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2176 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 2127 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1770 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1762 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 727 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 3FMC · CRYSTAL STRUCTURE OF a putative succinylglutamate desuccinylase / aspartoacylase family… · 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 A1S356
- Elsewhere: RCSB PDB 3FMC · PDBe 3FMC · UniProt A1S356
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.