MolNFT v1 · #137408 · protein
Crystal structure of SEC23A/SEC24A/SEC22 complexed with 4- phenylbutyric acid (50MM soaking)
5VNN · Protein transport protein SEC23A: “Crystal structure of SEC23A/SEC24A/SEC22 complexed with 4- phenylbutyric acid (50MM soaking)”. X-ray diffraction, 2 ligands (CLT, ZN), 20 pockets (best druggability 0.79). MolNFT v1 #137408 on…
- PDB
- 5VNN
- 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, O08547
- Ligands
- CLT, ZN
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport protein SEC23A | protein | 699 | 33% helix, 22% strand | Q15436 |
| B | Protein transport protein SEC24A | protein | 731 | 31% helix, 21% strand | O95486 |
| C | Vesicle-trafficking protein SEC22B | protein | 137 | 35% helix, 26% strand | O08547 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1020 | 0.79 | 0.81 | 94 | empty |
| 2 | 669 | 0.79 | 0.84 | 63 | empty |
| 3 | 201 | 0.75 | 0.91 | 42 | empty |
| 4 | 464 | 0.73 | 0.83 | 56 | empty |
| 5 | 292 | 0.68 | 0.84 | 38 | empty |
Interfaces
3 interfaces between chains.
- A–B · 968 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 779 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 454 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5VNN · Crystal structure of Sec23a/Sec24a/Sec22 complexed with 4-phenylbutyric acid (50mM… · 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
- O08547 · AlphaFold monomer V2.0 prediction for vesicle-trafficking protein SEC22B (O08547) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 O08547
- Elsewhere: RCSB PDB 5VNN · PDBe 5VNN · UniProt Q15436 · UniProt O95486 · UniProt O08547
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