Research workbench
The crystal structure of an adenylate kinase-related protein bound to AMP from sulfolobus solfataricus to 2.3A
Analyse The crystal structure of an adenylate kinase-related protein bound to AMP from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LW7
- Type
- protein
- Length
- 340 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate kinase related protein (adka-like)
- UniProt
- D0KU01
- Ligands
- AMP
- Pockets
- 5 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylate kinase related protein (adka-like) | protein | 170 | 58% helix, 14% strand | D0KU01 |
| B | Adenylate kinase related protein (adka-like) | protein | 170 | 59% helix, 15% strand | D0KU01 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 191 | 0.54 | 0.79 | 24 | empty |
| 2 | 146 | 0.53 | 0.80 | 27 | AMP |
| 3 | 187 | 0.47 | 0.75 | 29 | empty |
| 4 | 96 | 0.38 | 0.75 | 17 | empty |
| 5 | 96 | 0.37 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 867 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3LW7 · The Crystal Structure of an Adenylate kinase-related protein bound to AMP from sulfolobus… · 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
- Every structure of UniProt D0KU01
- Elsewhere: RCSB PDB 3LW7 · PDBe 3LW7 · UniProt D0KU01
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