Research workbench
Crystal structure of SEC23A/SEC24A/SEC22 complexed with 4- phenylbutyric acid (15MM soaking)
Analyse Crystal structure of SEC23A/SEC24A/SEC22 complexed with 4- phenylbutyric acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VNM
- Type
- protein
- Length
- 1,566 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 0.81
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 | 698 | 33% helix, 24% strand | Q15436 |
| B | Protein transport protein SEC24A | protein | 731 | 30% helix, 21% strand | O95486 |
| C | Vesicle-trafficking protein SEC22B | protein | 137 | 37% 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 716 | 0.81 | 0.85 | 68 | empty |
| 2 | 1057 | 0.77 | 0.79 | 93 | CLT |
| 3 | 212 | 0.75 | 0.90 | 39 | empty |
| 4 | 399 | 0.72 | 0.83 | 44 | empty |
| 5 | 271 | 0.68 | 0.84 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–B · 952 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 806 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 392 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5VNM · Crystal structure of Sec23a/Sec24a/Sec22 complexed with 4-phenylbutyric acid (15mM… · 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 0.99
- 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 5VNM · PDBe 5VNM · UniProt Q15436 · UniProt O95486 · UniProt O08547
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