Research workbench
Adenylate kinase from methanococcus igneus - AMP bound form
Analyse Adenylate kinase from methanococcus igneus - AMP bound form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PJW
- Type
- protein
- Length
- 2,292 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate kinase
- EC
- 2.7.4.3
- UniProt
- P43408
- Ligands
- AMP, MG
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Adenylate kinase (EC 2.7.4.3) | protein | 191 | 53% helix, 18% strand | P43408 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.77 | 0.90 | 40 | AMP, MG |
| 2 | 269 | 0.76 | 0.89 | 41 | AMP, MG |
| 3 | 343 | 0.75 | 0.87 | 52 | AMP, MG |
| 4 | 414 | 0.75 | 0.85 | 62 | AMP, MG |
| 5 | 896 | 0.75 | 0.79 | 87 | AMP, MG |
Interfaces
27 interfaces between chains.
- D–E · 860 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 858 Ų buried · 7 hydrogen bonds · protein-protein
- K–L · 857 Ų buried · 7 hydrogen bonds · protein-protein
- H–I · 856 Ų buried · 7 hydrogen bonds · protein-protein
- J–K · 849 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6PJW · Adenylate kinase from Methanococcus igneus - AMP bound form · the same entry in another collection · chain L against L, 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 P43408
- Elsewhere: RCSB PDB 6PJW · PDBe 6PJW · UniProt P43408
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