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New structural conformations of adenylate kinase from Streptococcus pneumoniae D39
Analyse New structural conformations of adenylate kinase from Streptococcus pneumoniae… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4W5H
- Type
- protein
- Length
- 208 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.96
- Source
- Streptococcus pneumoniae D39
- Molecule
- Adenylate kinase
- EC
- 2.7.4.3
- UniProt
- Q04ML5
- Pockets
- 1 · best druggability 0.61
Structure
x-ray diffraction · resolution 1.96 · 1 distinct chain · 55% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylate kinase (EC 2.7.4.3) | protein | 208 | 55% helix, 16% strand | Q04ML5 |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 170 | 0.61 | 0.83 | 28 | empty |
Compared structures
- 4W5H · New structural conformations of adenylate kinase from streptococcus pneumoniae D39 · 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 0.72
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 4W5H · PDBe 4W5H · UniProt Q04ML5
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