MolNFT v1 · #112341 · protein
Crystal structure of aspartate semialdehyde dehydrogenase with NADP from trichophyton rubrum
4ZIC: “Crystal structure of aspartate semialdehyde dehydrogenase with NADP from trichophyton rubrum”. X-ray diffraction, 2 ligands (NAP, SO4), 13 pockets (best druggability 0.80). MolNFT v1 #112341 on GenesisL1: 3D structure, binding sites…
- PDB
- 4ZIC
- Type
- protein
- Length
- 2,138 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate semialdehyde dehydrogenase
- EC
- 1.2.1.11
- Ligands
- NAP, SO4
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Aspartate semialdehyde dehydrogenase (EC 1.2.1.11) | protein | 356 | 31% helix, 22% strand | — |
| C, B, E, F | Aspartate semialdehyde dehydrogenase (EC 1.2.1.11) | protein | 357 | 31% helix, 21% strand | — |
| A | Aspartate semialdehyde dehydrogenase (EC 1.2.1.11) | protein | 354 | 34% helix, 22% strand | — |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains C, A
- SO4 · Sulfate ion · ion · 6 copies · chains D, C, A, B, E, F
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 | 716 | 0.80 | 0.84 | 81 | SO4 |
| 2 | 128 | 0.80 | 0.97 | 19 | empty |
| 3 | 676 | 0.79 | 0.84 | 90 | SO4 |
| 4 | 713 | 0.74 | 0.80 | 68 | SO4 |
| 5 | 627 | 0.74 | 0.81 | 68 | SO4 |
Interfaces
8 interfaces between chains.
- D–C · 1798 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1786 Ų buried · 43 hydrogen bonds · protein-protein
- C–A · 745 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 679 Ų buried · 6 hydrogen bonds · protein-protein
- D–B · 663 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4ZIC · Crystal Structure of Aspartate Semialdehyde Dehydrogenase with NADP from Trichophyton… · the same entry in another collection · chain D against D, 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
- Elsewhere: RCSB PDB 4ZIC · PDBe 4ZIC
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