Research workbench
Crystal structure of the ternary complex of sp-asadh with NADP and 1, 2,3-benzenetricarboxylic acid
Analyse Crystal structure of the ternary complex of sp-asadh with NADP and 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R3N
- 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
- Q8DQ00
- Ligands
- NAP, 3GQ, NA
- Pockets
- 4 · best druggability 0.67
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 | 34% helix, 23% strand | Q8DQ00 |
| B | Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) | protein | 347 | 35% helix, 24% strand | Q8DQ00 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains A, B
- 3GQ · benzene-1,2,3-tricarboxylic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- ACT · Acetate ion · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 448 | 0.67 | 0.80 | 48 | NAP, 3GQ, ACT |
| 2 | 414 | 0.66 | 0.79 | 39 | NAP, 3GQ, ACT |
| 3 | 128 | 0.41 | 0.75 | 23 | EDO |
| 4 | 119 | 0.40 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 2895 Ų buried · 61 hydrogen bonds · protein-protein
Compared structures
- 4R3N · Crystal structure of the ternary complex of sp-ASADH with NADP and… · 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 Q8DQ00
- Elsewhere: RCSB PDB 4R3N · PDBe 4R3N · UniProt Q8DQ00
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