MolNFT v1 · #105404 · protein
Complex crystal structure of 4-nitro-2-phosphono-benzoic acid with sp- aspartate-semialdehyde dehydrogenase and nicotinamide-dinucleotide
4R41: “Complex crystal structure of 4-nitro-2-phosphono-benzoic acid with sp- aspartate-semialdehyde dehydrogenase…”. X-ray diffraction, 3 ligands (4NO, NAP, NA), 4 pockets (best druggability 0.67). MolNFT v1 #105404 on GenesisL1: 3D…
- PDB
- 4R41
- 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
- 4NO, NAP, 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 | A5MTN0 |
| B | Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) | protein | 347 | 35% helix, 24% strand | A5MTN0 |
Ligands and binding sites
- 4NO · 4-nitro-2-phosphonobenzoic acid · ligand · 2 copies · chains A, B
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 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
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 | 423 | 0.67 | 0.80 | 51 | 4NO, NAP |
| 2 | 400 | 0.66 | 0.80 | 41 | 4NO |
| 3 | 144 | 0.43 | 0.75 | 23 | EDO |
| 4 | 137 | 0.43 | 0.75 | 25 | EDO |
Interfaces
1 interface between chains.
- A–B · 2896 Ų buried · 59 hydrogen bonds · protein-protein
Compared structures
- 4R41 · Complex Crystal structure of 4-nitro-2-phosphono-benzoic acid with… · 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 4R41 · PDBe 4R41 · UniProt A5MTN0
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