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Crystal structure of 3-mbt repeats of lethal (3) malignant brain tumor (seleno-met) at 1.85 ångström
Analyse Crystal structure of 3-mbt repeats of lethal (3) malignant brain tumor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OYX
- Type
- protein
- Length
- 939 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LETHAL(3)MALIGNANT brain tumor-like protein
- UniProt
- Q9Y468
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | LETHAL(3)MALIGNANT brain tumor-like protein | protein | 313 | 20% helix, 29% strand | Q9Y468 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 14 copies · chains A, B, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 7 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.73 | 0.76 | 90 | SO4 |
| 2 | 905 | 0.72 | 0.76 | 68 | SO4 |
| 3 | 723 | 0.72 | 0.78 | 54 | SO4 |
| 4 | 89 | 0.31 | 0.73 | 15 | SO4 |
Interfaces
2 interfaces between chains.
- A–C · 333 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 60 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 1OYX · Crystal structure of 3-mbt repeats of lethal (3) malignant brain tumor (seleno-met) at… · the same entry in another collection · chain C against C, TM-score 1.00
- Q9Y468 · AlphaFold monomer V2.0 prediction for LETHAL(3)MALIGNANT brain tumor- like protein 1… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9Y468
- Elsewhere: RCSB PDB 1OYX · PDBe 1OYX · UniProt Q9Y468
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