MolNFT v1 · #172793 · protein
Cryo-EM structure of human er membrane protein complex in gdn detergent
7ADP · Er membrane protein complex subunit 1: “Cryo-EM structure of human er membrane protein complex in gdn detergent”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.80). MolNFT v1 #172793 on GenesisL1: 3D…
- PDB
- 7ADP
- Type
- protein
- Length
- 1,880 residues
- Chains
- 8
- 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, O43402, Q5UCC4
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 8 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Er membrane protein complex subunit 1 | protein | 881 | 9% helix, 36% strand | Q8N766 |
| B | Er membrane protein complex subunit 2 | protein | 273 | 74% helix, 0% strand | Q15006 |
| C | Er membrane protein complex subunit 3 | protein | 191 | 58% helix, 1% strand | Q9P0I2 |
| D | Er membrane protein complex subunit 4 | protein | 44 | 11% helix, 9% strand | Q5J8M3 |
| E | Membrane magnesium transporter 1 | protein | 92 | 75% helix, 1% strand | Q8N4V1 |
| F | Er membrane protein complex subunit 6 | protein | 100 | 71% helix, 1% strand | Q9BV81 |
| H | Er membrane protein complex subunit 8 | protein | 166 | 42% helix, 19% strand | O43402 |
| I | Er membrane protein complex subunit 10 | protein | 133 | 12% helix, 39% strand | Q5UCC4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1140 | 0.80 | 0.81 | 118 | empty |
| 2 | 690 | 0.75 | 0.81 | 74 | empty |
| 3 | 382 | 0.75 | 0.85 | 36 | empty |
| 4 | 94 | 0.74 | 0.96 | 20 | empty |
| 5 | 80 | 0.73 | 0.96 | 23 | empty |
Interfaces
17 interfaces between chains.
- B–C · 1664 Ų buried · 24 hydrogen bonds · protein-protein
- B–E · 1553 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1472 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 1394 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1360 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7ADP · Cryo-EM structure of human ER membrane protein complex in GDN detergent · the same entry in another collection · chain I against I, TM-score 1.00
- 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 0.94
- Q5UCC4 · AlphaFold monomer V2.0 prediction for er membrane protein complex subunit 10 (Q5UCC4) · a predicted model of the same protein · chain I against A, TM-score 0.94
- 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 0.94
- Q15006 · AlphaFold monomer V2.0 prediction for er membrane protein complex subunit 2 (Q15006) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 O43402
- Every structure of UniProt Q5UCC4
- Elsewhere: RCSB PDB 7ADP · PDBe 7ADP · UniProt Q8N766 · UniProt Q15006 · UniProt Q9P0I2 · UniProt Q5J8M3 · UniProt Q8N4V1 · UniProt Q9BV81 · UniProt O43402 · UniProt Q5UCC4
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