Research workbench
Crystal structure of human er membrane protein complex subunits EMC2 and EMC9
Analyse Crystal structure of human er membrane protein complex subunits EMC2 and EMC9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y4L
- Type
- protein
- Length
- 456 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Er membrane protein complex subunit 2; Er membrane protein complex subunit 9
- UniProt
- Q15006, Q9Y3B6
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 64% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Er membrane protein complex subunit 2 | protein | 271 | 82% helix, 0% strand | Q15006 |
| B | Er membrane protein complex subunit 9 | protein | 185 | 37% helix, 23% strand | Q9Y3B6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 677 | 0.69 | 0.77 | 82 | EDO, SO4 |
| 2 | 116 | 0.49 | 0.80 | 15 | EDO |
| 3 | 69 | 0.46 | 0.83 | 17 | EDO |
| 4 | 111 | 0.44 | 0.77 | 16 | PEG |
| 5 | 73 | 0.43 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1144 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6Y4L · Crystal structure of human ER membrane protein complex subunits EMC2 and EMC9 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y3B6 · AlphaFold monomer V2.0 prediction for er membrane protein complex subunit 9 (Q9Y3B6) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q15006 · AlphaFold monomer V2.0 prediction for er membrane protein complex subunit 2 (Q15006) · a predicted model of the same protein · chain A against A, TM-score 0.75
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 Q15006
- Every structure of UniProt Q9Y3B6
- Elsewhere: RCSB PDB 6Y4L · PDBe 6Y4L · UniProt Q15006 · UniProt Q9Y3B6
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