Research workbench
Crystal structure of guanylate kinase from pseudomonas aeruginosa PAO1 in complex with gmp
Analyse Crystal structure of guanylate kinase from pseudomonas aeruginosa PAO1 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7U5F
- Type
- protein
- Length
- 792 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanylate kinase
- EC
- 2.7.4.8
- UniProt
- Q9HTM2
- Ligands
- 5GP, MG
- Pockets
- 14 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanylate kinase (EC 2.7.4.8) | protein | 197 | 47% helix, 22% strand | Q9HTM2 |
| B | Guanylate kinase (EC 2.7.4.8) | protein | 198 | 47% helix, 21% strand | Q9HTM2 |
| C | Guanylate kinase (EC 2.7.4.8) | protein | 198 | 51% helix, 21% strand | Q9HTM2 |
| D | Guanylate kinase (EC 2.7.4.8) | protein | 199 | 49% helix, 22% strand | Q9HTM2 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1001 | 0.70 | 0.75 | 123 | empty |
| 2 | 342 | 0.68 | 0.82 | 46 | 5GP |
| 3 | 265 | 0.68 | 0.84 | 42 | 5GP |
| 4 | 196 | 0.67 | 0.86 | 31 | 5GP |
| 5 | 248 | 0.65 | 0.83 | 35 | 5GP |
Interfaces
6 interfaces between chains.
- B–D · 1566 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1535 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 330 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 197 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 116 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7U5F · Crystal structure of guanylate kinase from Pseudomonas aeruginosa PAO1 in complex with GMP · the same entry in another collection · chain D against D, TM-score 1.00
- Q9HTM2 · AlphaFold monomer V2.0 prediction for guanylate kinase (Q9HTM2) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 Q9HTM2
- Elsewhere: RCSB PDB 7U5F · PDBe 7U5F · UniProt Q9HTM2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.