Research workbench
Crystal structure of PF10_0086, adenylate kinase from plasmodium falciparum
Analyse Crystal structure of PF10_0086, adenylate kinase from plasmodium falciparum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TLX
- Type
- protein
- Length
- 812 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate kinase 2
- EC
- 2.7.4.3
- UniProt
- Q7Z0H0
- Ligands
- ADP, AMP, ATP, MG
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylate kinase 2 (EC 2.7.4.3) | protein | 235 | 51% helix, 16% strand | Q7Z0H0 |
| B | Adenylate kinase 2 (EC 2.7.4.3) | protein | 240 | 51% helix, 16% strand | Q7Z0H0 |
| C | Adenylate kinase 2 (EC 2.7.4.3) | protein | 155 | 54% helix, 10% strand | Q7Z0H0 |
| D | Adenylate kinase 2 (EC 2.7.4.3) | protein | 182 | 54% helix, 13% strand | Q7Z0H0 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B
- AMP · Adenosine monophosphate · ligand · chains A
- ATP · Adenosine-5'-triphosphate · ligand · chains D
- 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
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 775 | 0.82 | 0.85 | 84 | AMP, ADP |
| 2 | 428 | 0.79 | 0.88 | 56 | ADP |
| 3 | 1105 | 0.75 | 0.77 | 88 | empty |
| 4 | 786 | 0.74 | 0.79 | 71 | empty |
| 5 | 555 | 0.68 | 0.78 | 78 | empty |
Interfaces
6 interfaces between chains.
- A–B · 552 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 369 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 335 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 313 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 259 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3TLX · Crystal Structure of PF10_0086, adenylate kinase from plasmodium falciparum · 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 Q7Z0H0
- Elsewhere: RCSB PDB 3TLX · PDBe 3TLX · UniProt Q7Z0H0
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