Research workbench
Adenylate kinase from methanococcus igneus - apo form
Analyse Adenylate kinase from methanococcus igneus - apo form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PK5
- Type
- protein
- Length
- 1,137 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
- CL
- Pockets
- 16 · best druggability 0.67
Structure
x-ray diffraction · 6 distinct chains · 52% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylate kinase (EC 2.7.4.3) | protein | 188 | 52% helix, 19% strand | P43408 |
| B | Adenylate kinase (EC 2.7.4.3) | protein | 189 | 52% helix, 19% strand | P43408 |
| C | Adenylate kinase (EC 2.7.4.3) | protein | 190 | 52% helix, 18% strand | P43408 |
| D | Adenylate kinase (EC 2.7.4.3) | protein | 191 | 51% helix, 18% strand | P43408 |
| E | Adenylate kinase (EC 2.7.4.3) | protein | 189 | 52% helix, 19% strand | P43408 |
| F | Adenylate kinase (EC 2.7.4.3) | protein | 190 | 51% helix, 18% strand | P43408 |
Ligands and binding sites
- CL · Chloride ion · ion · 15 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 601 | 0.67 | 0.77 | 55 | empty |
| 2 | 532 | 0.64 | 0.76 | 53 | CL |
| 3 | 516 | 0.64 | 0.76 | 60 | CL |
| 4 | 529 | 0.64 | 0.76 | 56 | CL |
| 5 | 591 | 0.62 | 0.74 | 60 | empty |
Interfaces
12 interfaces between chains.
- A–B · 819 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 816 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 813 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 803 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 798 Ų buried · 7 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 6PK5 · PDBe 6PK5 · UniProt P43408
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