MolNFT v1 · #62466 · protein
Crystal structure of the mammalian copii-coat protein SEC23A/24A complexed with the snare protein SEC22 and bound to the transport signal sequence of vesicular stomatitis virus glycoprotein
3EGD · Protein transport protein SEC23A: “Crystal structure of the mammalian copii-coat protein SEC23A/24A complexed with the snare protein SEC22 and…”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 3EGD
- Type
- protein
- Length
- 1,586 residues
- Chains
- 4
- 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 · 4 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport protein SEC23A | protein | 711 | 34% helix, 24% strand | Q15436 |
| B | Protein transport protein SEC24A | protein | 731 | 31% helix, 21% strand | O95486 |
| C | Vesicle-trafficking protein SEC22B | protein | 137 | 33% helix, 24% strand | O75396 |
| D | 10 residue peptide from vsv glycoprotein | protein | 7 | 0% helix, 0% strand | — |
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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 715 | 0.81 | 0.85 | 70 | empty |
| 2 | 1082 | 0.77 | 0.79 | 95 | empty |
| 3 | 196 | 0.76 | 0.91 | 40 | empty |
| 4 | 340 | 0.71 | 0.84 | 48 | empty |
| 5 | 372 | 0.71 | 0.82 | 44 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1000 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 791 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 471 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 420 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3EGD · Crystal structure of the mammalian COPII-coat protein Sec23a/24a complexed with the SNARE… · 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 0.99
- 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 3EGD · PDBe 3EGD · UniProt Q15436 · UniProt O95486 · UniProt O75396
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