Research workbench
Crystal structure of yeast SEC13/31 edge element of the copii vesicular coat, native version
Analyse Crystal structure of yeast SEC13/31 edge element of the copii vesicular coat… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PM6
- Type
- protein
- Length
- 1,259 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein transport protein SEC31; Protein transport protein SEC13
- UniProt
- P38968, Q04491
- Pockets
- 18 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport protein SEC31 | protein | 345 | 63% helix, 4% strand | P38968 |
| B | Protein transport protein SEC13 | protein | 279 | 2% helix, 51% strand | Q04491 |
| C | Protein transport protein SEC31 | protein | 347 | 64% helix, 5% strand | P38968 |
| D | Protein transport protein SEC13 | protein | 288 | 3% helix, 48% strand | Q04491 |
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1068 | 0.84 | 0.85 | 101 | empty |
| 2 | 952 | 0.84 | 0.85 | 89 | empty |
| 3 | 128 | 0.80 | 0.98 | 17 | empty |
| 4 | 128 | 0.80 | 0.97 | 19 | empty |
| 5 | 173 | 0.59 | 0.82 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–C · 3235 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2327 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2265 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 2PM6 · Crystal Structure of yeast Sec13/31 edge element of the COPII vesicular coat, native… · the same entry in another collection · chain D against D, 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 0.97
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 P38968
- Every structure of UniProt Q04491
- Elsewhere: RCSB PDB 2PM6 · PDBe 2PM6 · UniProt P38968 · UniProt Q04491
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