Research workbench
Cryo-EM structure of human er membrane protein complex in lipid nanodiscs
Analyse Cryo-EM structure of human er membrane protein complex in lipid nanodiscs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ADO
- Type
- protein
- Length
- 2,085 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Er membrane protein complex subunit 1; Er membrane protein complex subunit 2; Er membrane…
- UniProt
- Q8N766, Q15006, Q9P0I2, Q5J8M3, Q8N4V1, Q9BV81, Q9NPA0, O43402, Q5UCC4
- Ligands
- PCW, NAG
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 10 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Er membrane protein complex subunit 1 | protein | 915 | 10% helix, 38% strand | Q8N766 |
| B | Er membrane protein complex subunit 2 | protein | 275 | 75% helix, 0% strand | Q15006 |
| C | Er membrane protein complex subunit 3 | protein | 203 | 58% helix, 2% strand | Q9P0I2 |
| D | Er membrane protein complex subunit 4 | protein | 64 | 30% helix, 9% strand | Q5J8M3 |
| E | Membrane magnesium transporter 1 | protein | 97 | 69% helix, 1% strand | Q8N4V1 |
| F | Er membrane protein complex subunit 6 | protein | 100 | 71% helix, 0% strand | Q9BV81 |
| G | Er membrane protein complex subunit 7 | protein | 97 | 7% helix, 22% strand | Q9NPA0 |
| H | Er membrane protein complex subunit 8 | protein | 176 | 39% helix, 21% strand | O43402 |
| I | Er membrane protein complex subunit 10 | protein | 142 | 14% helix, 39% strand | Q5UCC4 |
| K | Unassigned helix | protein | 16 | 88% helix, 0% strand | — |
Ligands and binding sites
- PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 5 copies · chains A, C, E, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, D, G, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 737 | 0.79 | 0.83 | 99 | empty |
| 2 | 1108 | 0.77 | 0.79 | 95 | empty |
| 3 | 132 | 0.77 | 0.95 | 21 | empty |
| 4 | 432 | 0.75 | 0.85 | 35 | empty |
| 5 | 134 | 0.75 | 0.94 | 29 | empty |
Interfaces
20 interfaces between chains.
- A–C · 1673 Ų buried · 11 hydrogen bonds · protein-protein
- A–I · 1661 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1638 Ų buried · 25 hydrogen bonds · protein-protein
- A–G · 1616 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 1549 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 7ADO · Cryo-EM structure of human ER membrane protein complex in lipid nanodiscs · the same entry in another collection · chain K against K, TM-score 1.00
- Q8N766 · AlphaFold monomer V2.0 prediction for er membrane protein complex subunit 1 (Q8N766) · a predicted model of the same protein · chain A against A, TM-score 0.96
- O43402 · AlphaFold monomer V2.0 prediction for er membrane protein complex subunit 8 (O43402) · a predicted model of the same protein · chain H against A, TM-score 0.96
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 Q8N766
- Every structure of UniProt Q15006
- Every structure of UniProt Q9P0I2
- Every structure of UniProt Q5J8M3
- Every structure of UniProt Q8N4V1
- Every structure of UniProt Q9BV81
- Every structure of UniProt Q9NPA0
- Every structure of UniProt O43402
- Every structure of UniProt Q5UCC4
- Elsewhere: RCSB PDB 7ADO · PDBe 7ADO · UniProt Q8N766 · UniProt Q15006 · UniProt Q9P0I2 · UniProt Q5J8M3 · UniProt Q8N4V1 · UniProt Q9BV81 · UniProt Q9NPA0 · UniProt O43402 · UniProt Q5UCC4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.