Research workbench
Crystal structure of the human SEC23A/24A heterodimer, complexed with the snare protein SEC22B
Analyse Crystal structure of the human SEC23A/24A heterodimer, complexed with the snare… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NUP
- Type
- protein
- Length
- 1,567 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein transport protein SEC23A; Protein transport protein SEC24A; Vesicle-trafficking…
- UniProt
- Q15436, O95486, O75396
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport protein SEC23A | protein | 699 | 33% helix, 25% strand | Q15436 |
| B | Protein transport protein SEC24A | protein | 731 | 31% helix, 21% strand | O95486 |
| C | Vesicle-trafficking protein SEC22B | protein | 137 | 34% helix, 25% strand | O75396 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.81 | 0.83 | 118 | empty |
| 2 | 828 | 0.81 | 0.84 | 81 | empty |
| 3 | 428 | 0.73 | 0.83 | 49 | empty |
| 4 | 322 | 0.70 | 0.84 | 36 | empty |
| 5 | 324 | 0.68 | 0.82 | 47 | empty |
Interfaces
3 interfaces between chains.
- A–B · 999 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 809 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 442 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2NUP · Crystal Structure of the human Sec23a/24a heterodimer, complexed with the SNARE protein… · the same entry in another collection · chain A against A, TM-score 1.00
- Q15436 · AlphaFold monomer V2.0 prediction for protein transport protein SEC23A (Q15436) · a predicted model of the same protein · chain A against A, TM-score 1.00
- O95486 · AlphaFold monomer V2.0 prediction for protein transport protein SEC24A (O95486) · a predicted model of the same protein · chain B against A, TM-score 0.98
- O75396 · AlphaFold monomer V2.0 prediction for vesicle-trafficking protein SEC22B (O75396) · 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 Q15436
- Every structure of UniProt O95486
- Every structure of UniProt O75396
- Elsewhere: RCSB PDB 2NUP · PDBe 2NUP · UniProt Q15436 · UniProt O95486 · UniProt O75396
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