Research workbench
Trappcore plus C8 (355-596) and C11 (1-718) from minitrappiii
Analyse Trappcore plus C8 (355-596) and C11 (1-718) from minitrappiii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B70
- Type
- protein
- Length
- 2,112 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trafficking protein particle complex subunit; GEO08327P1; Probable trafficking protein…
- UniProt
- Q9VSY8, Q9VF82, Q9VA95, Q9VLI9, Q9VUZ1, Q7K2Q8, A1Z8I0, Q9VW22, Q8IRE3
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 10 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trafficking protein particle complex subunit | protein | 165 | 46% helix, 15% strand | Q9VSY8 |
| B | GEO08327P1 | protein | 151 | 30% helix, 7% strand | Q9VF82 |
| C | Trafficking protein particle complex subunit | protein | 145 | 34% helix, 19% strand | Q9VA95 |
| D | Trafficking protein particle complex subunit | protein | 219 | 24% helix, 27% strand | Q9VLI9 |
| E | Probable trafficking protein particle complex subunit 2 | protein | 139 | 45% helix, 17% strand | Q9VUZ1 |
| F | Trafficking protein particle complex subunit 5 | protein | 164 | 52% helix, 13% strand | Q7K2Q8 |
| G | Trafficking protein particle complex subunit | protein | 169 | 47% helix, 15% strand | Q9VSY8 |
| H | TRAPPC2L | protein | 138 | 32% helix, 20% strand | A1Z8I0 |
| I | FI18195P1 | protein | 208 | 78% helix, 0% strand | Q9VW22 |
| J | Trafficking protein particle complex subunit 11 | protein | 614 | 55% helix, 4% strand | Q8IRE3 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 346 | 0.81 | 0.90 | 66 | empty |
| 2 | 247 | 0.80 | 0.92 | 40 | empty |
| 3 | 100 | 0.79 | 0.98 | 27 | empty |
| 4 | 263 | 0.78 | 0.90 | 44 | empty |
| 5 | 166 | 0.76 | 0.92 | 31 | empty |
Interfaces
15 interfaces between chains.
- C–D · 1779 Ų buried · 42 hydrogen bonds · protein-protein
- F–G · 1366 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1268 Ų buried · 7 hydrogen bonds · protein-protein
- B–H · 1153 Ų buried · 24 hydrogen bonds · protein-protein
- D–G · 997 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7B70 · TRAPPCore plus C8 (355-596) and C11 (1-718) from MiniTRAPPIII · the same entry in another collection · chain J against J, TM-score 1.00
- Q9VUZ1 · AlphaFold monomer V2.0 prediction for probable trafficking protein particle complex… · a predicted model of the same protein · chain E against A, TM-score 0.92
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 Q9VSY8
- Every structure of UniProt Q9VF82
- Every structure of UniProt Q9VA95
- Every structure of UniProt Q9VLI9
- Every structure of UniProt Q9VUZ1
- Every structure of UniProt Q7K2Q8
- Every structure of UniProt A1Z8I0
- Every structure of UniProt Q9VW22
- Every structure of UniProt Q8IRE3
- Elsewhere: RCSB PDB 7B70 · PDBe 7B70 · UniProt Q9VSY8 · UniProt Q9VF82 · UniProt Q9VA95 · UniProt Q9VLI9 · UniProt Q9VUZ1 · UniProt Q7K2Q8 · UniProt A1Z8I0 · UniProt Q9VW22 · UniProt Q8IRE3
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