MolNFT v1 · #168954 · protein
Structure of the human er membrane protein complex in a lipid nanodisc
6WW7 · Er membrane protein complex subunit 1: “Structure of the human er membrane protein complex in a lipid nanodisc”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.79). MolNFT v1 #168954 on GenesisL1: 3D structure…
- PDB
- 6WW7
- Type
- protein
- Length
- 2,074 residues
- Chains
- 9
- 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, Q8N4V1, Q9BV81, Q9NPA0, O43402, Q5UCC4
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 9 distinct chains · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Er membrane protein complex subunit 1 | protein | 927 | 9% helix, 45% strand | Q8N766 |
| B | Er membrane protein complex subunit 2 | protein | 281 | 76% helix, 0% strand | Q15006 |
| C | Er membrane protein complex subunit 3 | protein | 209 | 57% helix, 2% strand | Q9P0I2 |
| D | Er membrane protein complex subunit 4 | protein | 14 | 0% helix, 57% strand | — |
| E | Membrane magnesium transporter 1 | protein | 101 | 59% helix, 1% strand | Q8N4V1 |
| F | Er membrane protein complex subunit 6 | protein | 99 | 75% helix, 1% strand | Q9BV81 |
| G | Er membrane protein complex subunit 7 | protein | 111 | 5% helix, 42% strand | Q9NPA0 |
| H | Er membrane protein complex subunit 8 | protein | 182 | 36% helix, 23% strand | O43402 |
| I | Er membrane protein complex subunit 10 | protein | 150 | 19% helix, 42% strand | Q5UCC4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, I, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.79 | 0.81 | 83 | empty |
| 2 | 1200 | 0.79 | 0.81 | 128 | empty |
| 3 | 255 | 0.75 | 0.89 | 33 | empty |
| 4 | 612 | 0.73 | 0.81 | 68 | empty |
| 5 | 1169 | 0.73 | 0.76 | 60 | empty |
Interfaces
16 interfaces between chains.
- A–G · 1811 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1795 Ų buried · 25 hydrogen bonds · protein-protein
- A–I · 1743 Ų buried · 19 hydrogen bonds · protein-protein
- B–E · 1670 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1642 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 6WW7 · Structure of the human ER membrane protein complex in a lipid nanodisc · the same entry in another collection · chain I against I, 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 0.97
- 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
- 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 0.95
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 Q8N4V1
- Every structure of UniProt Q9BV81
- Every structure of UniProt Q9NPA0
- Every structure of UniProt O43402
- Every structure of UniProt Q5UCC4
- Elsewhere: RCSB PDB 6WW7 · PDBe 6WW7 · UniProt Q8N766 · UniProt Q15006 · UniProt Q9P0I2 · UniProt Q8N4V1 · UniProt Q9BV81 · UniProt Q9NPA0 · UniProt O43402 · UniProt Q5UCC4
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