MolNFT v1 · #100422 · protein
Crystal structure of adenylosuccinate lyase from leishmania donovani
4MX2: “Crystal structure of adenylosuccinate lyase from leishmania donovani”. X-ray diffraction, 2 ligands (AMP, SO4), 20 pockets (best druggability 0.89). MolNFT v1 #100422 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4MX2
- Type
- protein
- Length
- 3,449 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylosuccinate lyase
- UniProt
- A7LBL3
- Ligands
- AMP, SO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 8 distinct chains · 64% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylosuccinate lyase | protein | 424 | 65% helix, 5% strand | A7LBL3 |
| B | Adenylosuccinate lyase | protein | 439 | 64% helix, 5% strand | A7LBL3 |
| C | Adenylosuccinate lyase | protein | 426 | 65% helix, 5% strand | A7LBL3 |
| D | Adenylosuccinate lyase | protein | 439 | 63% helix, 5% strand | A7LBL3 |
| E | Adenylosuccinate lyase | protein | 425 | 63% helix, 5% strand | A7LBL3 |
| F | Adenylosuccinate lyase | protein | 431 | 63% helix, 5% strand | A7LBL3 |
| G | Adenylosuccinate lyase | protein | 427 | 64% helix, 5% strand | A7LBL3 |
| H | Adenylosuccinate lyase | protein | 438 | 63% helix, 5% strand | A7LBL3 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 8 copies · chains A, B, E, F, C, D, G, H
- SO4 · Sulfate ion · ion · 3 copies · chains C, D, G, H
- GOL · Glycerol · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.89 | 0.90 | 102 | empty |
| 2 | 607 | 0.85 | 0.90 | 77 | empty |
| 3 | 467 | 0.84 | 0.91 | 43 | empty |
| 4 | 643 | 0.81 | 0.86 | 95 | empty |
| 5 | 953 | 0.77 | 0.80 | 75 | AMP, SO4 |
Interfaces
14 interfaces between chains.
- D–H · 3725 Ų buried · 82 hydrogen bonds · protein-protein
- B–F · 3697 Ų buried · 77 hydrogen bonds · protein-protein
- C–G · 3574 Ų buried · 75 hydrogen bonds · protein-protein
- A–E · 3549 Ų buried · 74 hydrogen bonds · protein-protein
- C–D · 3126 Ų buried · 53 hydrogen bonds · protein-protein
Compared structures
- 4MX2 · Crystal Structure of adenylosuccinate lyase from Leishmania donovani · 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 A7LBL3
- Elsewhere: RCSB PDB 4MX2 · PDBe 4MX2 · UniProt A7LBL3
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