MolNFT v1 · #36376 · protein
Crystal structure of E.COLI guanylate kinase in complex with AP5G
2F3R: “Crystal structure of E.COLI guanylate kinase in complex with AP5G”. X-ray diffraction, 1 ligand (G5P), 5 pockets (best druggability 0.69). MolNFT v1 #36376 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2F3R
- Type
- protein
- Length
- 400 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanylate kinase
- EC
- 2.7.4.8
- UniProt
- P60546
- Ligands
- G5P
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanylate kinase (EC 2.7.4.8) | protein | 201 | 48% helix, 21% strand | P60546 |
| B | Guanylate kinase (EC 2.7.4.8) | protein | 199 | 42% helix, 21% strand | P60546 |
Ligands and binding sites
- G5P · P1-(5'-adenosyl)-P5-(5'-guanosyl) pentaphosphate · 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 | 428 | 0.69 | 0.80 | 44 | G5P |
| 2 | 493 | 0.67 | 0.78 | 49 | G5P |
| 3 | 153 | 0.41 | 0.74 | 30 | empty |
| 4 | 120 | 0.37 | 0.74 | 17 | empty |
| 5 | 83 | 0.36 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1528 Ų buried · 14 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 P60546
- Elsewhere: RCSB PDB 2F3R · PDBe 2F3R · UniProt P60546
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