Research workbench
Crystal structure of an N-succinylglutamate 5-semialdehyde dehydrogenase from burkholderia thailandensis
Analyse Crystal structure of an N-succinylglutamate 5-semialdehyde dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KNA
- Type
- protein
- Length
- 973 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-succinylglutamate 5-semialdehyde dehydrogenase
- EC
- 1.2.1.71
- UniProt
- Q2SXN9
- Ligands
- CA, CL
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-succinylglutamate 5-semialdehyde dehydrogenase (EC 1.2.1.71) | protein | 487 | 39% helix, 22% strand | Q2SXN9 |
| B | N-succinylglutamate 5-semialdehyde dehydrogenase (EC 1.2.1.71) | protein | 486 | 39% helix, 23% strand | Q2SXN9 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.76 | 0.84 | 84 | CL, EDO, CA |
| 2 | 61 | 0.73 | 0.99 | 21 | empty |
| 3 | 495 | 0.72 | 0.81 | 52 | empty |
| 4 | 472 | 0.71 | 0.81 | 53 | empty |
| 5 | 326 | 0.63 | 0.79 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 3827 Ų buried · 50 hydrogen bonds · protein-protein
Compared structures
- 4KNA · Crystal structure of an N-succinylglutamate 5-semialdehyde dehydrogenase from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q2SXN9 · AlphaFold monomer V2.0 prediction for N-succinylglutamate 5-semialdehyde dehydrogenase… · a predicted model of the same protein · chain B 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 Q2SXN9
- Elsewhere: RCSB PDB 4KNA · PDBe 4KNA · UniProt Q2SXN9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.