Research workbench
Crystal structure of E.COLI guanylate kinase in complex with ganciclovir monophosphate
Analyse Crystal structure of E.COLI guanylate kinase in complex with ganciclovir… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F3T
- Type
- protein
- Length
- 1,223 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanylate kinase
- EC
- 2.7.4.8
- UniProt
- P60546
- Ligands
- LGP
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F | Guanylate kinase (EC 2.7.4.8) | protein | 205 | 45% helix, 21% strand | P60546 |
| B | Guanylate kinase (EC 2.7.4.8) | protein | 203 | 45% helix, 22% strand | P60546 |
| C | Guanylate kinase (EC 2.7.4.8) | protein | 201 | 46% helix, 22% strand | P60546 |
| E | Guanylate kinase (EC 2.7.4.8) | protein | 204 | 45% helix, 22% strand | P60546 |
Ligands and binding sites
- LGP · N9-1-hydroxy-prop-2-oxymethyl-guanine-3'-monophosphate · ligand · 4 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 823 | 0.85 | 0.88 | 86 | empty |
| 2 | 722 | 0.85 | 0.89 | 84 | empty |
| 3 | 618 | 0.84 | 0.89 | 75 | empty |
| 4 | 123 | 0.69 | 0.91 | 21 | empty |
| 5 | 311 | 0.56 | 0.76 | 43 | empty |
Interfaces
15 interfaces between chains.
- C–D · 1637 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1636 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1624 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 718 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 641 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2F3T · Crystal Structure Of E.coli Guanylate Kinase In Complex With Ganciclovir monophosphate · the same entry in another collection · chain F against F, TM-score 1.00
- P60546 · AlphaFold monomer V2.0 prediction for guanylate kinase (P60546) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 2F3T · PDBe 2F3T · UniProt P60546
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