Research workbench
Molecular mechanism and evolution of guanylate kinase regulation by (P)PPGPP
Analyse Molecular mechanism and evolution of guanylate kinase regulation by (P)PPGPP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QRH
- Type
- protein
- Length
- 735 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanylate kinase
- EC
- 2.7.4.8
- UniProt
- W6E076
- Ligands
- 0O2, MG, K, SO4
- Pockets
- 10 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanylate kinase (EC 2.7.4.8) | protein | 180 | 43% helix, 24% strand | W6E076 |
| B | Guanylate kinase (EC 2.7.4.8) | protein | 186 | 44% helix, 22% strand | W6E076 |
| C | Guanylate kinase (EC 2.7.4.8) | protein | 185 | 45% helix, 22% strand | W6E076 |
| D | Guanylate kinase (EC 2.7.4.8) | protein | 184 | 43% helix, 23% strand | W6E076 |
Ligands and binding sites
- 0O2 · guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate) · ligand · 3 copies · chains B, C, D
- MG · Magnesium ion · metal · 3 copies · chains B, C, D
- K · Potassium ion · metal · 3 copies · chains B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 625 | 0.65 | 0.75 | 79 | empty |
| 2 | 160 | 0.53 | 0.80 | 28 | MG, K, 0O2 |
| 3 | 154 | 0.52 | 0.80 | 25 | MG, 0O2 |
| 4 | 163 | 0.51 | 0.78 | 29 | MG, 0O2 |
| 5 | 177 | 0.47 | 0.76 | 26 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1310 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1310 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 218 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 215 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 93 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4QRH · Molecular mechanism and evolution of guanylate kinase regulation by (p)ppGpp · the same entry in another collection · chain A against A, TM-score 1.00
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 W6E076
- Elsewhere: RCSB PDB 4QRH · PDBe 4QRH · UniProt W6E076
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