MolNFT v1 · #62443 · protein
Crystal structure of the mammalian copii-coat protein SEC23/24 bound to the transport signal sequence of syntaxin 5
3EFO · Protein transport protein SEC23A: “Crystal structure of the mammalian copii-coat protein SEC23/24 bound to the transport signal sequence of…”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.78). MolNFT v1 #62443…
- PDB
- 3EFO
- Type
- protein
- Length
- 1,490 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein transport protein SEC23A; SEC24 related gene family, member D; Peptide
- UniProt
- Q15436, Q8IYI7
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport protein SEC23A | protein | 716 | 35% helix, 23% strand | Q15436 |
| B | SEC24 related gene family, member D | protein | 767 | 33% helix, 21% strand | Q8IYI7 |
| C | Peptide | protein | 7 | 0% helix, 57% 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 735 | 0.78 | 0.82 | 79 | empty |
| 2 | 495 | 0.76 | 0.84 | 55 | empty |
| 3 | 384 | 0.72 | 0.84 | 46 | empty |
| 4 | 418 | 0.68 | 0.80 | 51 | empty |
| 5 | 483 | 0.67 | 0.78 | 47 | empty |
Interfaces
2 interfaces between chains.
- A–B · 725 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 520 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3EFO · Crystal Structure of the mammalian COPII-coat protein Sec23/24 bound to the transport… · 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
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 Q8IYI7
- Elsewhere: RCSB PDB 3EFO · PDBe 3EFO · UniProt Q15436 · UniProt Q8IYI7
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