MolNFT v1 · #107060 · protein
Crystal structure of an adenylate kinase mutant--AKM1
4TYP: “Crystal structure of an adenylate kinase mutant--AKM1”. X-ray diffraction, 2 ligands (AP5, ZN), 8 pockets (best druggability 0.80). MolNFT v1 #107060 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4TYP
- Type
- protein
- Length
- 790 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate kinase
- EC
- 2.7.4.3
- UniProt
- P16304
- Ligands
- AP5, ZN
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Adenylate kinase (EC 2.7.4.3) | protein | 190 | 56% helix, 14% strand | P16304 |
| B | Adenylate kinase (EC 2.7.4.3) | protein | 206 | 53% helix, 17% strand | P16304 |
| A | Adenylate kinase (EC 2.7.4.3) | protein | 208 | 52% helix, 15% strand | P16304 |
| D | Adenylate kinase (EC 2.7.4.3) | protein | 186 | 55% helix, 15% strand | P16304 |
Ligands and binding sites
- AP5 · Bis(adenosine)-5'-pentaphosphate · ligand · 4 copies · chains C, B, A, D
- ZN · Zinc ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 540 | 0.80 | 0.87 | 56 | AP5 |
| 2 | 882 | 0.80 | 0.82 | 75 | AP5 |
| 3 | 538 | 0.80 | 0.86 | 58 | AP5 |
| 4 | 591 | 0.79 | 0.85 | 62 | AP5 |
| 5 | 195 | 0.49 | 0.76 | 18 | empty |
Interfaces
2 interfaces between chains.
- B–D · 542 Ų buried · 10 hydrogen bonds · protein-protein
- C–B · 333 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
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 P16304
- Elsewhere: RCSB PDB 4TYP · PDBe 4TYP · UniProt P16304
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