MolNFT v1 · #32642 · protein
Structure of adenylate kinase 5
2BWJ: “Structure of adenylate kinase 5”. X-ray diffraction, 3 ligands (AMP, SO4, CL), 17 pockets (best druggability 0.65). MolNFT v1 #32642 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2BWJ
- Type
- protein
- Length
- 1,160 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate kinase 5
- EC
- 2.7.4.3
- UniProt
- Q9Y6K8
- Ligands
- AMP, SO4, CL
- Pockets
- 17 · best druggability 0.65
Structure
x-ray diffraction · 6 distinct chains · 59% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylate kinase 5 (EC 2.7.4.3) | protein | 196 | 61% helix, 13% strand | Q9Y6K8 |
| B | Adenylate kinase 5 (EC 2.7.4.3) | protein | 195 | 59% helix, 12% strand | Q9Y6K8 |
| C | Adenylate kinase 5 (EC 2.7.4.3) | protein | 193 | 60% helix, 13% strand | Q9Y6K8 |
| D | Adenylate kinase 5 (EC 2.7.4.3) | protein | 192 | 60% helix, 13% strand | Q9Y6K8 |
| E | Adenylate kinase 5 (EC 2.7.4.3) | protein | 190 | 58% helix, 14% strand | Q9Y6K8 |
| F | Adenylate kinase 5 (EC 2.7.4.3) | protein | 194 | 57% helix, 13% strand | Q9Y6K8 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 3 copies · chains B, C, F
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 5 copies · chains A, F, B, E, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 329 | 0.65 | 0.81 | 37 | SO4, CL |
| 2 | 308 | 0.65 | 0.81 | 44 | SO4, CL |
| 3 | 319 | 0.64 | 0.80 | 43 | SO4 |
| 4 | 284 | 0.63 | 0.80 | 33 | SO4 |
| 5 | 315 | 0.63 | 0.79 | 36 | SO4 |
Interfaces
5 interfaces between chains.
- C–F · 1387 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1322 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1313 Ų buried · 20 hydrogen bonds · protein-protein
- A–E · 491 Ų buried · 2 hydrogen bonds · protein-protein
- A–F · 461 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
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 Q9Y6K8
- Elsewhere: RCSB PDB 2BWJ · PDBe 2BWJ · UniProt Q9Y6K8
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