MolNFT v1 · #101523 · protein
Crystal structure of adenylate kinase from streptococcus pneumoniae with AP5A
4NU0: “Crystal structure of adenylate kinase from streptococcus pneumoniae with AP5A”. X-ray diffraction, 2 ligands (AP5, MG), 5 pockets (best druggability 0.81). MolNFT v1 #101523 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4NU0
- Type
- protein
- Length
- 424 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate kinase
- EC
- 2.7.4.3
- UniProt
- Q04ML5
- Ligands
- AP5, MG
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenylate kinase (EC 2.7.4.3) | protein | 212 | 53% helix, 16% strand | Q04ML5 |
Ligands and binding sites
- 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
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 488 | 0.81 | 0.88 | 57 | MG, AP5 |
| 2 | 520 | 0.80 | 0.87 | 62 | MG, AP5 |
| 3 | 125 | 0.62 | 0.86 | 22 | empty |
| 4 | 94 | 0.56 | 0.85 | 24 | empty |
| 5 | 181 | 0.45 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 155 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4NU0 · Crystal structure of Adenylate kinase from Streptococcus pneumoniae with Ap5A · the same entry in another collection · chain A against A, TM-score 1.00
- Q04ML5 · AlphaFold monomer V2.0 prediction for adenylate kinase (Q04ML5) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q04ML5
- Elsewhere: RCSB PDB 4NU0 · PDBe 4NU0 · UniProt Q04ML5
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