Research workbench
SEC13/SEC31 edge element, loop deletion mutant
Analyse SEC13/SEC31 edge element, loop deletion mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MZL
- Type
- protein
- Length
- 2,432 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein transport protein SEC13; Protein transport protein SEC31
- UniProt
- Q04491, P38968
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Protein transport protein SEC13 | protein | 279 | 0% helix, 52% strand | Q04491 |
| B, D, F, H | Protein transport protein SEC31 | protein | 329 | 64% helix, 4% strand | P38968 |
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 | 1174 | 0.84 | 0.85 | 108 | empty |
| 2 | 1113 | 0.83 | 0.84 | 102 | empty |
| 3 | 1008 | 0.83 | 0.84 | 88 | empty |
| 4 | 1085 | 0.82 | 0.83 | 86 | empty |
| 5 | 141 | 0.80 | 0.97 | 16 | empty |
Interfaces
11 interfaces between chains.
- F–H · 5401 Ų buried · 47 hydrogen bonds · protein-protein
- B–D · 5311 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 1804 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1790 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 1763 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3MZL · Sec13/Sec31 edge element, loop deletion mutant · the same entry in another collection · chain H against H, TM-score 1.00
- Q04491 · AlphaFold monomer V2.0 prediction for protein transport protein SEC13 (Q04491) · a predicted model of the same protein · chain A 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 B against A, TM-score 0.70
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 Q04491
- Every structure of UniProt P38968
- Elsewhere: RCSB PDB 3MZL · PDBe 3MZL · UniProt Q04491 · UniProt P38968
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