Research workbench
Human osgep / LAGE3 / GON7 complex
Analyse Human osgep / LAGE3 / GON7 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GWJ
- Type
- protein
- Length
- 466 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EKC/KEOPS complex subunit LAGE3; EKC/KEOPS complex subunit GON7; Probable tRNA…
- EC
- 2.3.1.234
- UniProt
- Q14657, Q9BXV9, Q9NPF4
- Ligands
- MG
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | EKC/KEOPS complex subunit LAGE3 | protein | 84 | 43% helix, 29% strand | Q14657 |
| D | EKC/KEOPS complex subunit GON7 | protein | 48 | 42% helix, 25% strand | Q9BXV9 |
| K | Probable tRNA N6-adenosine threonylcarbamoyltransferase (EC 2.3.1.234) | protein | 334 | 48% helix, 20% strand | Q9NPF4 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains K
- GOL · Glycerol · additive · 5 copies · chains B, D, K
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains K, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 422 | 0.71 | 0.82 | 55 | GOL |
| 2 | 209 | 0.63 | 0.83 | 29 | GOL |
| 3 | 128 | 0.44 | 0.77 | 21 | empty |
Interfaces
2 interfaces between chains.
- B–D · 1173 Ų buried · 8 hydrogen bonds · protein-protein
- B–K · 1080 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6GWJ · Human OSGEP / LAGE3 / GON7 complex · the same entry in another collection · chain B against B, TM-score 1.00
- Q9NPF4 · AlphaFold monomer V2.0 prediction for probable tRNA N6-adenosine… · a predicted model of the same protein · chain K against A, TM-score 0.99
- Q14657 · AlphaFold monomer V2.0 prediction for EKC/KEOPS complex subunit LAGE3 (Q14657) · a predicted model of the same protein · chain B against A, TM-score 0.92
- Q9BXV9 · AlphaFold monomer V2.0 prediction for EKC/KEOPS complex subunit GON7 (Q9BXV9) · a predicted model of the same protein · chain D against A, TM-score 0.76
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 Q14657
- Every structure of UniProt Q9BXV9
- Every structure of UniProt Q9NPF4
- Elsewhere: RCSB PDB 6GWJ · PDBe 6GWJ · UniProt Q14657 · UniProt Q9BXV9 · UniProt Q9NPF4
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