Research workbench
Crystal structure of adenylate kinase ancestor 4 with zn and AMP-ADP bound
Analyse Crystal structure of adenylate kinase ancestor 4 with zn and AMP-ADP bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5G40
- Type
- protein
- Length
- 215 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate kinse
- EC
- 2.7.4.3
- Ligands
- ADP, AMP, ZN
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylate kinse (EC 2.7.4.3) | protein | 215 | 51% helix, 17% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- AMP · Adenosine monophosphate · ligand · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.79 | 0.88 | 58 | ADP, AMP |
| 2 | 59 | 0.45 | 0.84 | 22 | empty |
| 3 | 73 | 0.36 | 0.76 | 10 | empty |
Compared structures
- 5G40 · Crystal structure of adenylate kinase ancestor 4 with Zn and AMP-ADP bound · 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 5G40 · PDBe 5G40
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