Research workbench
Adenylate kinase from methanococcus igneus - AP5A bound form
Analyse Adenylate kinase from methanococcus igneus - AP5A bound form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PSP
- Type
- protein
- Length
- 1,146 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate kinase
- EC
- 2.7.4.3
- UniProt
- P43408
- Ligands
- AP5
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Adenylate kinase (EC 2.7.4.3) | protein | 191 | 52% helix, 18% strand | P43408 |
Ligands and binding sites
- AP5 · Bis(adenosine)-5'-pentaphosphate · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.80 | 0.90 | 43 | AP5 |
| 2 | 318 | 0.80 | 0.90 | 39 | AP5 |
| 3 | 326 | 0.79 | 0.90 | 45 | AP5 |
| 4 | 330 | 0.79 | 0.89 | 37 | AP5 |
| 5 | 335 | 0.79 | 0.89 | 40 | AP5 |
Interfaces
12 interfaces between chains.
- E–F · 848 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 841 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 838 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 837 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 825 Ų buried · 8 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 P43408
- Elsewhere: RCSB PDB 6PSP · PDBe 6PSP · UniProt P43408
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