MolNFT v1 · #119692 · protein
Crystal structure of adenylate kinase ancestor 3 with zn, mg and AP5A bound
5G3Z · Adenylate kinse: “Crystal structure of adenylate kinase ancestor 3 with zn, mg and AP5A bound”. X-ray diffraction, 3 ligands (AP5, ZN, MG), 2 pockets (best druggability 0.80). MolNFT v1 #119692 on GenesisL1: 3D structure, binding…
- PDB
- 5G3Z
- 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
- AP5, ZN, MG
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylate kinse (EC 2.7.4.3) | protein | 215 | 52% helix, 17% strand | — |
Ligands and binding sites
- AP5 · Bis(adenosine)-5'-pentaphosphate · ligand · chains A
- ZN · Zinc ion · metal · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 579 | 0.80 | 0.86 | 66 | AP5, MG |
| 2 | 51 | 0.32 | 0.77 | 8 | empty |
Compared structures
- 5G3Z · Crystal structure of adenylate kinase ancestor 3 with Zn, Mg and Ap5A 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 5G3Z · PDBe 5G3Z
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