Research workbench
Crystal structure of SEC23 and TANGO1 PEPTIDE3 complex
Analyse Crystal structure of SEC23 and TANGO1 PEPTIDE3 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KYW
- Type
- protein
- Length
- 1,483 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein transport protein SEC23A; Protein transport protein SEC24D; TANGO1 PEPTIDE3
- UniProt
- Q15436, O94855
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.77
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 | 714 | 34% helix, 24% strand | Q15436 |
| B | Protein transport protein SEC24D | protein | 766 | 31% helix, 20% strand | O94855 |
| C | TANGO1 PEPTIDE3 | protein | 3 | 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 699 | 0.77 | 0.82 | 76 | empty |
| 2 | 393 | 0.72 | 0.84 | 45 | empty |
| 3 | 494 | 0.69 | 0.80 | 56 | empty |
| 4 | 462 | 0.69 | 0.80 | 56 | empty |
| 5 | 238 | 0.66 | 0.84 | 30 | empty |
Interfaces
2 interfaces between chains.
- A–B · 745 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 221 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5KYW · crystal structure of Sec23 and TANGO1 peptide3 complex · the same entry in another collection · chain A against A, TM-score 1.00
- O94855 · AlphaFold monomer V2.0 prediction for protein transport protein SEC24D (O94855) · a predicted model of the same protein · chain B 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 O94855
- Elsewhere: RCSB PDB 5KYW · PDBe 5KYW · UniProt Q15436 · UniProt O94855
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