Research workbench
Crystal structure of human adenylosuccinate lyase in complex with AMP
Analyse Crystal structure of human adenylosuccinate lyase in complex with AMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J91
- Type
- protein
- Length
- 1,832 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylosuccinate lyase
- EC
- 4.3.2.2
- UniProt
- P30566
- Ligands
- AMP, CL
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylosuccinate lyase (EC 4.3.2.2) | protein | 457 | 70% helix, 4% strand | P30566 |
| B | Adenylosuccinate lyase (EC 4.3.2.2) | protein | 463 | 68% helix, 4% strand | P30566 |
| C | Adenylosuccinate lyase (EC 4.3.2.2) | protein | 456 | 69% helix, 4% strand | P30566 |
| D | Adenylosuccinate lyase (EC 4.3.2.2) | protein | 456 | 69% helix, 4% strand | P30566 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, C, D, B
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 442 | 0.85 | 0.92 | 50 | GOL |
| 2 | 680 | 0.81 | 0.85 | 77 | GOL, AMP |
| 3 | 469 | 0.79 | 0.87 | 72 | empty |
| 4 | 1124 | 0.78 | 0.80 | 109 | AMP |
| 5 | 433 | 0.78 | 0.87 | 51 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3785 Ų buried · 79 hydrogen bonds · protein-protein
- C–D · 3753 Ų buried · 77 hydrogen bonds · protein-protein
- A–D · 2548 Ų buried · 54 hydrogen bonds · protein-protein
- B–C · 2510 Ų buried · 53 hydrogen bonds · protein-protein
- B–D · 1963 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 2J91 · Crystal structure of Human Adenylosuccinate Lyase in complex with AMP · the same entry in another collection · chain D against D, TM-score 1.00
- P30566 · AlphaFold monomer V2.0 prediction for adenylosuccinate lyase (P30566) · a predicted model of the same protein · 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 P30566
- Elsewhere: RCSB PDB 2J91 · PDBe 2J91 · UniProt P30566
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