MolNFT v1 · #171408 · protein
Structure of canine SEC61 inhibited by mycolactone
6Z3T · Protein transport protein SEC61 subunit alpha isoform 1: “Structure of canine SEC61 inhibited by mycolactone”. Electron microscopy, 1 ligand (Q6B), 8 pockets (best druggability 0.73). MolNFT v1 #171408 on GenesisL1: 3D structure…
- PDB
- 6Z3T
- Type
- protein
- Length
- 461 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein transport protein SEC61 subunit alpha isoform 1; Protein transport protein SEC61…
- UniProt
- P38377, P60058
- Ligands
- Q6B
- Pockets
- 8 · best druggability 0.73
Structure
electron microscopy · 3 distinct chains · 60% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport protein SEC61 subunit alpha isoform 1 | protein | 382 | 55% helix, 3% strand | P38377 |
| B | Protein transport protein SEC61 subunit gamma | protein | 59 | 80% helix, 2% strand | P60058 |
| C | Protein transport protein SEC61 subunit beta | protein | 20 | 90% helix, 0% strand | — |
Ligands and binding sites
- Q6B · [(6~{S},7~{S},9~{Z},12~{R})-12-[(~{Z},2~{S},6~{R}, 7~{R},9~{R})-4,6-dimethyl-7,9-bis(oxidanyl)dec-4-en-2-yl]-7,9-dimethyl-2-oxidanylidene-1-oxacyclododec-9-en-6-yl] (2~{E},4~{E},6~{E},8~{E},10~{E},12~{S},13~{S}, 15~{S})-4,6,10-trimethyl-12,13,15-tris(oxidanyl) hexadeca-2,4,6,8,10-pentaenoate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 779 | 0.73 | 0.78 | 80 | empty |
| 2 | 755 | 0.73 | 0.78 | 87 | empty |
| 3 | 147 | 0.52 | 0.80 | 25 | empty |
| 4 | 189 | 0.49 | 0.76 | 23 | empty |
| 5 | 99 | 0.39 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1547 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 291 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 33 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6Z3T · Structure of canine Sec61 inhibited by mycolactone · the same entry in another collection · chain A against A, TM-score 1.00
- P38377 · AlphaFold monomer V2.0 prediction for protein transport protein SEC61 subunit alpha… · a predicted model of the same protein · chain A against A, TM-score 0.92
- P60058 · AlphaFold monomer V2.0 prediction for protein transport protein SEC61 subunit gamma… · a predicted model of the same protein · chain B against A, TM-score 0.84
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 P38377
- Every structure of UniProt P60058
- Elsewhere: RCSB PDB 6Z3T · PDBe 6Z3T · UniProt P38377 · UniProt P60058
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