Research workbench
Complex crystal structure of sp-Aspartate-Semialdehyde-Dehydrogenase with 3-carboxy-ethyl-phthalic acid
Analyse Complex crystal structure of sp-Aspartate-Semialdehyde-Dehydrogenase with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R54
- Type
- protein
- Length
- 714 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.81
- Source
- Streptococcus pneumoniae
- Molecule
- Aspartate-semialdehyde dehydrogenase
- EC
- 1.2.1.11
- UniProt
- A5MTN0
- Ligands
- NAP, 3JM, NA
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · resolution 1.81 · 1 distinct chain · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) | protein | 357 | 34% helix, 23% strand | A5MTN0 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains A, B
- 3JM · 3-(2-carboxyethyl)benzene-1,2-dicarboxylic acid · ligand · chains A
- NA · Sodium ion · metal · 3 copies · chains A, B
- ACT · Acetate ion · additive · 2 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 | 398 | 0.66 | 0.80 | 38 | NAP, ACT |
| 2 | 416 | 0.66 | 0.79 | 37 | NAP, ACT, 3JM |
| 3 | 134 | 0.42 | 0.75 | 23 | empty |
| 4 | 127 | 0.41 | 0.75 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 2900 Ų buried · 59 hydrogen bonds · protein-protein
Compared structures
- 4R54 · Complex crystal structure of sp-aspartate-semialdehyde-dehydrogenase 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 4R54 · PDBe 4R54 · UniProt A5MTN0
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