Research workbench
Crystal structure of guanylate kinase from anaplasma phagocytophilum
Analyse Crystal structure of guanylate kinase from anaplasma phagocytophilum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LNC
- Type
- protein
- Length
- 376 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanylate kinase
- EC
- 2.7.4.8
- UniProt
- Q2GLF7
- Ligands
- 5GP
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanylate kinase (EC 2.7.4.8) | protein | 188 | 42% helix, 26% strand | Q2GLF7 |
| B | Guanylate kinase (EC 2.7.4.8) | protein | 188 | 43% helix, 23% strand | Q2GLF7 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 388 | 0.62 | 0.77 | 41 | 5GP |
| 2 | 353 | 0.61 | 0.78 | 40 | 5GP |
| 3 | 134 | 0.43 | 0.76 | 21 | empty |
| 4 | 110 | 0.34 | 0.73 | 22 | empty |
| 5 | 64 | 0.31 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1665 Ų buried · 17 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 Q2GLF7
- Elsewhere: RCSB PDB 3LNC · PDBe 3LNC · UniProt Q2GLF7
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