MolNFT v1 · #125102 · protein
Crystal structure of SEC23 and TANGO1 PEPTIDE4 complex
5KYY · Protein transport protein SEC23A: “Crystal structure of SEC23 and TANGO1 PEPTIDE4 complex”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.78). MolNFT v1 #125102 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5KYY
- Type
- protein
- Length
- 1,483 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein transport protein SEC23A; Protein transport protein SEC24D
- UniProt
- Q15436, O94855
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport protein SEC23A | protein | 716 | 33% helix, 23% strand | Q15436 |
| B | Protein transport protein SEC24D | protein | 767 | 31% helix, 20% strand | O94855 |
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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1088 | 0.78 | 0.80 | 108 | empty |
| 2 | 450 | 0.73 | 0.83 | 44 | empty |
| 3 | 498 | 0.70 | 0.80 | 61 | empty |
| 4 | 542 | 0.68 | 0.78 | 47 | empty |
| 5 | 397 | 0.68 | 0.81 | 51 | empty |
Interfaces
1 interface between chains.
- A–B · 737 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5KYY · Crystal structure of Sec23 and TANGO1 peptide4 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 5KYY · PDBe 5KYY · UniProt Q15436 · UniProt O94855
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