Research workbench
Crystal structure of aspartate beta-semialdehide dehydrogenase from streptococcus pneumoniae with 2',5'-adenosine diphosphate and D-2- aminoadipate
Analyse Crystal structure of aspartate beta-semialdehide dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PWK
- Type
- protein
- Length
- 716 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
- 25A, L14, NA
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 23% 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 | 359 | 34% helix, 23% strand | A5MTN0 |
Ligands and binding sites
- 25A · 5'-O-monophosphoryladenylyl(2'->5')adenylyl(2'->5') adenosine · ligand · 2 copies · chains A, B
- L14 · trans-cyclohexane-1,4-dicarboxylic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
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 | 400 | 0.67 | 0.81 | 38 | L14 |
| 2 | 441 | 0.67 | 0.79 | 54 | 25A, L14 |
| 3 | 131 | 0.44 | 0.76 | 26 | EDO |
| 4 | 128 | 0.42 | 0.75 | 25 | EDO |
| 5 | 58 | 0.28 | 0.74 | 18 | 25A |
Interfaces
1 interface between chains.
- A–B · 2913 Ų buried · 65 hydrogen bonds · protein-protein
Compared structures
- 3PWK · Crystal Structure of Aspartate beta-Semialdehide Dehydrogenase from Streptococcus… · 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 3PWK · PDBe 3PWK · UniProt A5MTN0
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