Research workbench
The structure of the copii coat assembled on membranes
Analyse The structure of the copii coat assembled on membranes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BZJ
- Type
- protein
- Length
- 1,943 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein transport protein SEC31; Protein transport protein SEC13
- UniProt
- P38968, Q04491
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 24% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport protein SEC31 | protein | 691 | 32% helix, 19% strand | P38968 |
| B | Protein transport protein SEC13 | protein | 279 | 2% helix, 51% strand | Q04491 |
| C | Protein transport protein SEC31 | protein | 693 | 32% helix, 20% strand | P38968 |
| F | Protein transport protein SEC13 | protein | 280 | 2% helix, 43% strand | Q04491 |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1094 | 0.84 | 0.85 | 101 | empty |
| 2 | 576 | 0.82 | 0.87 | 48 | empty |
| 3 | 121 | 0.80 | 0.98 | 16 | empty |
| 4 | 462 | 0.79 | 0.87 | 60 | empty |
| 5 | 461 | 0.79 | 0.87 | 57 | empty |
Interfaces
3 interfaces between chains.
- A–C · 3228 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2891 Ų buried · 31 hydrogen bonds · protein-protein
- C–F · 2869 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 4BZJ · The structure of the COPII coat assembled on membranes · the same entry in another collection · chain F against F, TM-score 1.00
- Q04491 · AlphaFold monomer V2.0 prediction for protein transport protein SEC13 (Q04491) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P38968 · AlphaFold monomer V2.0 prediction for protein transport protein SEC31 (P38968) · a predicted model of the same protein · chain C 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 P38968
- Every structure of UniProt Q04491
- Elsewhere: RCSB PDB 4BZJ · PDBe 4BZJ · UniProt P38968 · UniProt Q04491
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