MolNFT v1 · #188677 · protein
Crystal structure of guanylate kinase from pseudomonas aeruginosa PAO1 in complex with gmp
7U5F: “Crystal structure of guanylate kinase from pseudomonas aeruginosa PAO1 in complex with gmp”. X-ray diffraction, 2 ligands (5GP, MG), 14 pockets (best druggability 0.70). MolNFT v1 #188677 on GenesisL1: 3D structure, binding sites…
- 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
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