MolNFT v1 · #75816 · protein
Crystals structure of aspartate beta-semialdehyde dehydrogenase from streptococcus pneumoniae with cysteamine bound covalently to cys 128
3Q1L: “Crystals structure of aspartate beta-semialdehyde dehydrogenase from streptococcus pneumoniae with cysteamine…”. X-ray diffraction, 1 ligand (DHL), 9 pockets (best druggability 0.66). MolNFT v1 #75816 on GenesisL1: 3D structure…
- PDB
- 3Q1L
- Type
- protein
- Length
- 1,429 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate beta-semialdehyde dehydrogenase
- EC
- 1.2.1.11
- UniProt
- Q8DQ00
- Ligands
- DHL
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartate beta-semialdehyde dehydrogenase (EC 1.2.1.11) | protein | 357 | 34% helix, 23% strand | Q8DQ00 |
| B, D | Aspartate beta-semialdehyde dehydrogenase (EC 1.2.1.11) | protein | 356 | 33% helix, 24% strand | Q8DQ00 |
| C | Aspartate beta-semialdehyde dehydrogenase (EC 1.2.1.11) | protein | 360 | 34% helix, 23% strand | Q8DQ00 |
Ligands and binding sites
- DHL · 2-amino-ethanethiol · ligand · 4 copies · chains A, B, C, D
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 | 437 | 0.66 | 0.79 | 50 | DHL |
| 2 | 354 | 0.63 | 0.79 | 43 | DHL |
| 3 | 404 | 0.63 | 0.78 | 45 | DHL |
| 4 | 676 | 0.63 | 0.73 | 61 | empty |
| 5 | 323 | 0.62 | 0.79 | 40 | DHL |
Interfaces
3 interfaces between chains.
- C–D · 2932 Ų buried · 64 hydrogen bonds · protein-protein
- A–B · 2930 Ų buried · 64 hydrogen bonds · protein-protein
- A–C · 302 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 3Q1L · Crystals Structure of Aspartate beta-Semialdehyde 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 Q8DQ00
- Elsewhere: RCSB PDB 3Q1L · PDBe 3Q1L · UniProt Q8DQ00
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