MolNFT v1 · #108392 · protein
New structural conformations of adenylate kinase from streptococcus pneumoniae D39 with AP5A
4W5J: “New structural conformations of adenylate kinase from streptococcus pneumoniae D39 with AP5A”. X-ray diffraction, 2 ligands (AP5, MG), 10 pockets (best druggability 0.84). MolNFT v1 #108392 on GenesisL1: 3D structure, binding sites…
- PDB
- 4W5J
- Type
- protein
- Length
- 844 residues
- Chains
- 4
- 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
- 10 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Adenylate kinase (EC 2.7.4.3) | protein | 211 | 54% helix, 16% strand | Q04ML5 |
Ligands and binding sites
- AP5 · Bis(adenosine)-5'-pentaphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.84 | 0.85 | 106 | MG, AP5 |
| 2 | 458 | 0.79 | 0.87 | 52 | MG, AP5 |
| 3 | 477 | 0.79 | 0.86 | 56 | MG, AP5 |
| 4 | 947 | 0.79 | 0.81 | 92 | MG, AP5 |
| 5 | 114 | 0.60 | 0.86 | 23 | empty |
Interfaces
4 interfaces between chains.
- A–B · 479 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 117 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 88 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 33 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4W5J · New structural conformations of adenylate kinase from Streptococcus pneumoniae D39 with… · 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 0.99
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 4W5J · PDBe 4W5J · UniProt Q04ML5
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