MolNFT v1 · #105401 · protein
Crystal structure analysis of the 1,2,3-tricarboxylate benzoic acid bound to sp-asadh-2'5'-ADP complex
4R3W · Aspartate-semialdehyde dehydrogenase: “Crystal structure analysis of the 1,2,3-tricarboxylate benzoic acid bound to sp-asadh-2'5'-ADP complex”. X-ray diffraction, 3 ligands (A2P, 3GQ, NA), 5 pockets (best druggability 0.68). MolNFT…
- PDB
- 4R3W
- Type
- protein
- Length
- 704 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate-semialdehyde dehydrogenase
- EC
- 1.2.1.11
- UniProt
- A5MTN0
- Ligands
- A2P, 3GQ, NA
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) | protein | 357 | 35% helix, 24% strand | A5MTN0 |
| B | Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) | protein | 347 | 35% helix, 24% strand | A5MTN0 |
Ligands and binding sites
- A2P · Adenosine-2'-5'-diphosphate · ligand · 2 copies · chains A, B
- 3GQ · benzene-1,2,3-tricarboxylic acid · ligand · chains A
- NA · Sodium ion · metal · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 426 | 0.68 | 0.80 | 50 | A2P |
| 2 | 410 | 0.66 | 0.80 | 38 | 3GQ, ACT |
| 3 | 132 | 0.42 | 0.75 | 24 | EDO |
| 4 | 132 | 0.41 | 0.74 | 22 | EDO |
| 5 | 55 | 0.30 | 0.75 | 9 | empty |
Interfaces
1 interface between chains.
- A–B · 2918 Ų buried · 58 hydrogen bonds · protein-protein
Compared structures
- 4R3W · Crystal Structure Analysis of the 1,2,3-tricarboxylate benzoic acid bound to… · 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 A5MTN0
- Elsewhere: RCSB PDB 4R3W · PDBe 4R3W · UniProt A5MTN0
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