Research workbench
Crystal structure of staphylococcus aureus guanylate monophosphate kinase
Analyse Crystal structure of staphylococcus aureus guanylate monophosphate kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J41
- Type
- protein
- Length
- 692 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanylate kinase
- EC
- 2.7.4.8
- UniProt
- Q5HGM3
- Ligands
- 5GP, K, SO4
- Pockets
- 14 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanylate kinase (EC 2.7.4.8) | protein | 167 | 40% helix, 25% strand | Q5HGM3 |
| B | Guanylate kinase (EC 2.7.4.8) | protein | 173 | 40% helix, 24% strand | Q5HGM3 |
| C | Guanylate kinase (EC 2.7.4.8) | protein | 174 | 40% helix, 24% strand | Q5HGM3 |
| D | Guanylate kinase (EC 2.7.4.8) | protein | 178 | 43% helix, 23% strand | Q5HGM3 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 3 copies · chains B, C, D
- K · Potassium ion · metal · 3 copies · chains B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.67 | 0.73 | 83 | empty |
| 2 | 160 | 0.53 | 0.80 | 24 | SO4, K, 5GP |
| 3 | 170 | 0.51 | 0.79 | 26 | 5GP |
| 4 | 167 | 0.50 | 0.78 | 28 | SO4, K, 5GP |
| 5 | 109 | 0.44 | 0.78 | 20 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1168 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 996 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 220 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 219 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 94 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2J41 · Crystal structure of Staphylococcus aureus guanylate monophosphate kinase · the same entry in another collection · chain D against D, TM-score 1.00
- Q5HGM3 · AlphaFold monomer V2.0 prediction for guanylate kinase (Q5HGM3) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q5HGM3
- Elsewhere: RCSB PDB 2J41 · PDBe 2J41 · UniProt Q5HGM3
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