MolNFT v1 · #181439 · protein
Crystal structure of guanylate kinase from bartonella henselae str. houston-1
7LUY: “Crystal structure of guanylate kinase from bartonella henselae str. houston-1”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.75). MolNFT v1 #181439 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7LUY
- Type
- protein
- Length
- 1,208 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanylate kinase
- EC
- 2.7.4.8
- UniProt
- Q6G439
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 46% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanylate kinase (EC 2.7.4.8) | protein | 207 | 45% helix, 21% strand | Q6G439 |
| B | Guanylate kinase (EC 2.7.4.8) | protein | 202 | 45% helix, 22% strand | Q6G439 |
| C | Guanylate kinase (EC 2.7.4.8) | protein | 204 | 46% helix, 22% strand | Q6G439 |
| D | Guanylate kinase (EC 2.7.4.8) | protein | 205 | 46% helix, 21% strand | Q6G439 |
| E | Guanylate kinase (EC 2.7.4.8) | protein | 200 | 46% helix, 22% strand | Q6G439 |
| F | Guanylate kinase (EC 2.7.4.8) | protein | 190 | 50% helix, 21% strand | Q6G439 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 606 | 0.75 | 0.82 | 58 | empty |
| 2 | 402 | 0.66 | 0.79 | 50 | SO4 |
| 3 | 416 | 0.64 | 0.78 | 51 | empty |
| 4 | 360 | 0.60 | 0.77 | 38 | empty |
| 5 | 368 | 0.56 | 0.75 | 37 | empty |
Interfaces
7 interfaces between chains.
- A–F · 1823 Ų buried · 22 hydrogen bonds · protein-protein
- B–E · 1767 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1753 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 640 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 113 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7LUY · Crystal Structure of guanylate kinase from Bartonella henselae str. Houston-1 · the same entry in another collection · chain F against F, TM-score 1.00
- Q6G439 · AlphaFold monomer V2.0 prediction for guanylate kinase (Q6G439) · a predicted model of the same protein · chain C 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 Q6G439
- Elsewhere: RCSB PDB 7LUY · PDBe 7LUY · UniProt Q6G439
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