Research workbench
Crystal structure of aspartate beta-semialdehide dehydrogenase from streptococcus pneumoniae with D-2,3-diaminopropionate
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
- 3PYL
- Type
- protein
- Length
- 1,429 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate-semialdehyde dehydrogenase
- EC
- 1.2.1.11
- UniProt
- A5MTN0
- Ligands
- 2RA
- Pockets
- 9 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) | protein | 358 | 34% helix, 23% strand | A5MTN0 |
| B | Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) | protein | 354 | 35% helix, 24% strand | A5MTN0 |
| C | Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) | protein | 361 | 34% helix, 23% strand | A5MTN0 |
| D | Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) | protein | 356 | 35% helix, 24% strand | A5MTN0 |
Ligands and binding sites
- 2RA · 3-amino-D-alanine · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 344 | 0.65 | 0.80 | 41 | 2RA |
| 2 | 372 | 0.64 | 0.79 | 41 | 2RA |
| 3 | 393 | 0.64 | 0.79 | 40 | empty |
| 4 | 714 | 0.64 | 0.74 | 60 | empty |
| 5 | 358 | 0.63 | 0.79 | 40 | 2RA |
Interfaces
3 interfaces between chains.
- C–D · 2958 Ų buried · 63 hydrogen bonds · protein-protein
- A–B · 2935 Ų buried · 63 hydrogen bonds · protein-protein
- A–C · 306 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3PYL · Crystal structure of aspartate beta-semialdehide dehydrogenase from Streptococcus… · the same entry in another collection · chain C against C, 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 3PYL · PDBe 3PYL · UniProt A5MTN0
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