MolNFT v1 · #168285 · protein
Structure of the S. cerevisiae er membrane complex
6WB9 · Endoplasmic reticulum membrane protein complex subunit 10: “Structure of the S. cerevisiae er membrane complex”. Electron microscopy, 2 ligands (POV, NAG), 20 pockets (best druggability 0.76). MolNFT v1 #168285 on GenesisL1: 3D…
- PDB
- 6WB9
- Type
- protein
- Length
- 1,771 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoplasmic reticulum membrane protein complex subunit 10; Er membrane protein complex…
- UniProt
- Q12025, P25574, P47133, P36039, P53073, P40540, Q12431, P39543
- Ligands
- POV, NAG
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 8 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | Endoplasmic reticulum membrane protein complex subunit 10 | protein | 117 | 0% helix, 49% strand | Q12025 |
| 1 | Er membrane protein complex subunit 1 | protein | 649 | 10% helix, 38% strand | P25574 |
| 2 | Er membrane protein complex subunit 2 | protein | 292 | 77% helix, 0% strand | P47133 |
| 3 | Er membrane protein complex subunit 3 | protein | 197 | 64% helix, 2% strand | P36039 |
| 4 | Er membrane protein complex subunit 4 | protein | 148 | 49% helix, 3% strand | P53073 |
| 5 | Er membrane protein complex subunit 5 | protein | 128 | 60% helix, 4% strand | P40540 |
| 6 | Er membrane protein complex subunit 6 | protein | 98 | 77% helix, 1% strand | Q12431 |
| 7 | Protein SOP4 | protein | 142 | 4% helix, 35% strand | P39543 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 2 copies · chains 3, 4, 6, 5
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains 1, 7
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 | 326 | 0.76 | 0.88 | 66 | empty |
| 2 | 858 | 0.76 | 0.80 | 85 | empty |
| 3 | 929 | 0.73 | 0.77 | 61 | empty |
| 4 | 668 | 0.72 | 0.79 | 56 | empty |
| 5 | 680 | 0.72 | 0.78 | 55 | POV |
Interfaces
17 interfaces between chains.
- 2–5 · 2513 Ų buried · 30 hydrogen bonds · protein-protein
- 1–3 · 1999 Ų buried · 9 hydrogen bonds · protein-protein
- 1–7 · 1875 Ų buried · 19 hydrogen bonds · protein-protein
- 2–3 · 1657 Ų buried · 17 hydrogen bonds · protein-protein
- 2–4 · 1601 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 6WB9 · Structure of the S. cerevisiae ER membrane complex · the same entry in another collection · chain 7 against 7, TM-score 1.00
- Q12431 · AlphaFold monomer V2.0 prediction for er membrane protein complex subunit 6 (Q12431) · a predicted model of the same protein · chain 6 against A, TM-score 0.98
- P25574 · AlphaFold monomer V2.0 prediction for er membrane protein complex subunit 1 (P25574) · a predicted model of the same protein · chain 1 against A, TM-score 0.94
- P47133 · AlphaFold monomer V2.0 prediction for er membrane protein complex subunit 2 (P47133) · a predicted model of the same protein · chain 2 against A, TM-score 0.93
- P39543 · AlphaFold monomer V2.0 prediction for protein SOP4 (P39543) · a predicted model of the same protein · chain 7 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 Q12025
- Every structure of UniProt P25574
- Every structure of UniProt P47133
- Every structure of UniProt P36039
- Every structure of UniProt P53073
- Every structure of UniProt P40540
- Every structure of UniProt Q12431
- Every structure of UniProt P39543
- Elsewhere: RCSB PDB 6WB9 · PDBe 6WB9 · UniProt Q12025 · UniProt P25574 · UniProt P47133 · UniProt P36039 · UniProt P53073 · UniProt P40540 · UniProt Q12431 · UniProt P39543
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