MolNFT v1 · #51631 · protein
Human adenylosuccinate lyase in complex with its substrate N6-(1,2-dicarboxyethyl)-AMP, and its products AMP and fumarate.
2VD6: “Human adenylosuccinate lyase in complex with its substrate N6-(1,2-dicarboxyethyl)-AMP, and its products AMP…”. X-ray diffraction, 4 ligands (AMP, FUM, 2SA), 20 pockets (best druggability 0.86). MolNFT v1 #51631 on GenesisL1: 3D…
- PDB
- 2VD6
- Type
- protein
- Length
- 1,841 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, FUM, 2SA, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylosuccinate lyase (EC 4.3.2.2) | protein | 461 | 70% helix, 4% strand | P30566 |
| B | Adenylosuccinate lyase (EC 4.3.2.2) | protein | 461 | 70% helix, 4% strand | P30566 |
| C | Adenylosuccinate lyase (EC 4.3.2.2) | protein | 457 | 69% helix, 4% strand | P30566 |
| D | Adenylosuccinate lyase (EC 4.3.2.2) | protein | 462 | 70% helix, 4% strand | P30566 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B, D, C
- FUM · Fumaric acid · ligand · 2 copies · chains A, B, D, C
- 2SA · 2-[9-(3,4-dihydroxy-5-phosphonooxymethyl-tetrahydro-furan-2-yl)-9H-purin-6-ylamino]-succinic acid · ligand · 2 copies · chains A, B, C, D
- CL · Chloride ion · ion · 7 copies · chains B, D, A, C
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.86 | 0.94 | 41 | empty |
| 2 | 437 | 0.86 | 0.93 | 38 | empty |
| 3 | 692 | 0.79 | 0.84 | 69 | 2SA, GOL, CL |
| 4 | 1172 | 0.77 | 0.79 | 108 | AMP, FUM, GOL |
| 5 | 1142 | 0.77 | 0.79 | 102 | AMP, FUM, GOL, CL |
Interfaces
6 interfaces between chains.
- A–B · 3752 Ų buried · 75 hydrogen bonds · protein-protein
- C–D · 3743 Ų buried · 74 hydrogen bonds · protein-protein
- A–D · 2561 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 2538 Ų buried · 58 hydrogen bonds · protein-protein
- A–C · 1893 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 2VD6 · Human adenylosuccinate lyase in complex with its substrate N6-(1,2- Dicarboxyethyl)-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 C against A, TM-score 0.99
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 2VD6 · PDBe 2VD6 · UniProt P30566
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