MolNFT v1 · #84090 · protein
Crystal structure of pyrene-conjugated adenylate kinase
3X2S: “Crystal structure of pyrene-conjugated adenylate kinase”. X-ray diffraction, 3 ligands (JPY, AP5, MG), 6 pockets (best druggability 0.81). MolNFT v1 #84090 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3X2S
- Type
- protein
- Length
- 428 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate kinase
- EC
- 2.7.4.3
- UniProt
- H0QBG3
- Ligands
- JPY, AP5, MG
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenylate kinase (EC 2.7.4.3) | protein | 214 | 47% helix, 16% strand | H0QBG3 |
Ligands and binding sites
- JPY · N-(pyren-1-ylmethyl)acetamide · ligand · 4 copies · chains A, B
- AP5 · Bis(adenosine)-5'-pentaphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 486 | 0.81 | 0.88 | 81 | AP5, MG |
| 2 | 498 | 0.80 | 0.87 | 80 | AP5, MG |
| 3 | 109 | 0.41 | 0.76 | 32 | empty |
| 4 | 56 | 0.30 | 0.75 | 16 | empty |
| 5 | 56 | 0.29 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 509 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 3X2S · Crystal structure of pyrene-conjugated adenylate kinase · 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 H0QBG3
- Elsewhere: RCSB PDB 3X2S · PDBe 3X2S · UniProt H0QBG3
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