Research workbench
Crystal structure of neanderthal adenylosuccinate lyase (ADSL)IN complex with its products aicar and fumarate
Analyse Crystal structure of neanderthal adenylosuccinate lyase (ADSL)IN complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NXA
- Type
- protein
- Length
- 3,609 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylosuccinate lyase
- EC
- 4.3.2.2
- Ligands
- SSS, FUM, AMZ, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 8 distinct chains · 68% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylosuccinate lyase (EC 4.3.2.2) | protein | 464 | 69% helix, 4% strand | — |
| B | Adenylosuccinate lyase (EC 4.3.2.2) | protein | 415 | 68% helix, 5% strand | — |
| C | Adenylosuccinate lyase (EC 4.3.2.2) | protein | 418 | 67% helix, 5% strand | — |
| D | Adenylosuccinate lyase (EC 4.3.2.2) | protein | 440 | 66% helix, 4% strand | — |
| E | Adenylosuccinate lyase (EC 4.3.2.2) | protein | 466 | 66% helix, 4% strand | — |
| F | Adenylosuccinate lyase (EC 4.3.2.2) | protein | 466 | 69% helix, 4% strand | — |
| G | Adenylosuccinate lyase (EC 4.3.2.2) | protein | 463 | 69% helix, 4% strand | — |
| H | Adenylosuccinate lyase (EC 4.3.2.2) | protein | 477 | 68% helix, 4% strand | — |
Ligands and binding sites
- SSS · N-{[5-amino-1-(5-O-phosphono-beta-D-arabinofuranosyl)-1H-imidazol-4-yl]carbonyl}-L-aspartic acid · ligand · 6 copies · chains A, B, D, C, E, F, G, H
- FUM · Fumaric acid · ligand · 2 copies · chains B, C, D, E, G, H
- AMZ · Aminoimidazole 4-carboxamide ribonucleotide · ligand · 2 copies · chains B, C, D, E, G, H
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
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 | 1171 | 0.87 | 0.88 | 116 | SSS |
| 2 | 608 | 0.83 | 0.88 | 81 | FUM, AMZ |
| 3 | 596 | 0.83 | 0.88 | 81 | FUM, AMZ |
| 4 | 743 | 0.82 | 0.86 | 79 | empty |
| 5 | 558 | 0.82 | 0.88 | 50 | empty |
Interfaces
14 interfaces between chains.
- G–H · 4303 Ų buried · 77 hydrogen bonds · protein-protein
- E–F · 4005 Ų buried · 76 hydrogen bonds · protein-protein
- C–D · 3849 Ų buried · 73 hydrogen bonds · protein-protein
- A–B · 3729 Ų buried · 74 hydrogen bonds · protein-protein
- E–H · 3504 Ų buried · 64 hydrogen bonds · protein-protein
Compared structures
- 5NXA · Crystal structure of Neanderthal Adenylosuccinate Lyase (ADSL)in complex with its… · 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
- Elsewhere: RCSB PDB 5NXA · PDBe 5NXA
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