Research workbench
Bacterial TRNA(HIS) guanylyltransferase (THG1)-like protein in complex with ATP
Analyse Bacterial TRNA(HIS) guanylyltransferase (THG1)-like protein in complex with ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KGM
- Type
- protein
- Length
- 911 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- THG1-like uncharacterized protein
- UniProt
- Q3F0V8
- Ligands
- ATP, MG, PO4
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | THG1-like uncharacterized protein | protein | 230 | 48% helix, 18% strand | Q3F0V8 |
| B | THG1-like uncharacterized protein | protein | 228 | 50% helix, 17% strand | Q3F0V8 |
| C | THG1-like uncharacterized protein | protein | 229 | 46% helix, 19% strand | Q3F0V8 |
| D | THG1-like uncharacterized protein | protein | 224 | 46% helix, 21% strand | Q3F0V8 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 689 | 0.70 | 0.77 | 59 | ATP, MG |
| 2 | 225 | 0.66 | 0.84 | 28 | ATP |
| 3 | 179 | 0.62 | 0.84 | 28 | ATP |
| 4 | 176 | 0.61 | 0.83 | 31 | ATP, MG |
| 5 | 277 | 0.55 | 0.77 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2017 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1999 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 114 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 91 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 49 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4KGM · Bacterial tRNA(HIS) Guanylyltransferase (Thg1)-Like Protein in complex with ATP · 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 Q3F0V8
- Elsewhere: RCSB PDB 4KGM · PDBe 4KGM · UniProt Q3F0V8
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