Research workbench
Crystal structure of the scm-SAM and sfmbt-SAM heterodimer
Analyse Crystal structure of the scm-SAM and sfmbt-SAM heterodimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J8Y
- Type
- protein
- Length
- 295 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polycomb protein scm; Polycomb protein sfmbt
- UniProt
- Q9VHA0, Q9VK33
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Polycomb protein scm | protein | 78 | 68% helix, 0% strand | Q9VHA0 |
| C | Polycomb protein sfmbt | protein | 69 | 71% helix, 0% strand | Q9VK33 |
| D | Polycomb protein sfmbt | protein | 70 | 73% helix, 0% strand | Q9VK33 |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.80 | 0.96 | 29 | empty |
| 2 | 120 | 0.44 | 0.77 | 19 | empty |
| 3 | 135 | 0.41 | 0.75 | 22 | empty |
| 4 | 94 | 0.39 | 0.76 | 14 | empty |
| 5 | 91 | 0.35 | 0.74 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–C · 587 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 572 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 381 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 367 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 336 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5J8Y · Crystal structure of the Scm-SAM and Sfmbt-SAM heterodimer · the same entry in another collection · chain A against A, TM-score 1.00
- Q9VK33 · AlphaFold monomer V2.0 prediction for polycomb protein sfmbt (Q9VK33) · a predicted model of the same protein · chain C against A, TM-score 0.97
- Q9VHA0 · AlphaFold monomer V2.0 prediction for polycomb protein scm (Q9VHA0) · a predicted model of the same protein · chain A against A, TM-score 0.89
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 Q9VHA0
- Every structure of UniProt Q9VK33
- Elsewhere: RCSB PDB 5J8Y · PDBe 5J8Y · UniProt Q9VHA0 · UniProt Q9VK33
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.