Research workbench
Structure of the yeast trappiii-YPT1(RAB1) complex
Analyse Structure of the yeast trappiii-YPT1(RAB1) complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KMT
- Type
- protein
- Length
- 1,838 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trafficking protein particle complex subunit 23; Trafficking protein particle complex…
- UniProt
- Q03784, Q03337, Q03630, P36149, Q99394, P38334, P01123, P46944
- Ligands
- PLM
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 8 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Trafficking protein particle complex subunit 23 | protein | 169 | 32% helix, 21% strand | Q03784 |
| J | Trafficking protein particle complex subunit 31 | protein | 191 | 47% helix, 14% strand | Q03337 |
| G | Trafficking protein particle complex subunit BET5 | protein | 156 | 36% helix, 20% strand | Q03630 |
| I, F | Trafficking protein particle complex subunit BET3 | protein | 182 | 52% helix, 15% strand | P36149 |
| E | Trafficking protein particle complex subunit 33 | protein | 178 | 45% helix, 11% strand | Q99394 |
| K | Trafficking protein particle complex subunit 20 | protein | 131 | 40% helix, 18% strand | P38334 |
| A | GTP-binding protein YPT1 | protein | 174 | 32% helix, 27% strand | P01123 |
| B | Trafficking protein particle complex III-specific subunit 85 | protein | 475 | 58% helix, 8% strand | P46944 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 2 copies · chains H, I, F, E
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 | 209 | 0.83 | 0.96 | 34 | PLM |
| 2 | 206 | 0.83 | 0.95 | 34 | PLM |
| 3 | 932 | 0.74 | 0.78 | 78 | empty |
| 4 | 118 | 0.74 | 0.93 | 21 | empty |
| 5 | 134 | 0.66 | 0.88 | 26 | empty |
Interfaces
16 interfaces between chains.
- F–E · 2061 Ų buried · 22 hydrogen bonds · protein-protein
- J–I · 1784 Ų buried · 18 hydrogen bonds · protein-protein
- J–K · 1777 Ų buried · 33 hydrogen bonds · protein-protein
- H–G · 1565 Ų buried · 21 hydrogen bonds · protein-protein
- H–I · 1313 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 lipid (palmitoylation).
Compared structures
- 7KMT · Structure of the yeast TRAPPIII-Ypt1(Rab1) complex · the same entry in another collection · chain B against B, TM-score 1.00
- P46944 · AlphaFold monomer V2.0 prediction for trafficking protein particle complex III-specific… · a predicted model of the same protein · chain B against A, TM-score 0.98
- P36149 · AlphaFold monomer V2.0 prediction for trafficking protein particle complex subunit BET3… · a predicted model of the same protein · chain F against A, TM-score 0.97
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 Q03784
- Every structure of UniProt Q03337
- Every structure of UniProt Q03630
- Every structure of UniProt P36149
- Every structure of UniProt Q99394
- Every structure of UniProt P38334
- Every structure of UniProt P01123
- Every structure of UniProt P46944
- Elsewhere: RCSB PDB 7KMT · PDBe 7KMT · UniProt Q03784 · UniProt Q03337 · UniProt Q03630 · UniProt P36149 · UniProt Q99394 · UniProt P38334 · UniProt P01123 · UniProt P46944
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.