MolNFT v1 · #161412 · protein
Crystal structure of 14-3-3SIGMA in complex with a RAPGEF2 PT740 phosphopeptide
6QDT · 14-3-3 protein sigma: “Crystal structure of 14-3-3SIGMA in complex with a RAPGEF2 PT740 phosphopeptide”. X-ray diffraction, 3 ligands (NA, CA, CL), 2 pockets (best druggability 0.60). MolNFT v1 #161412 on GenesisL1: 3D structure…
- PDB
- 6QDT
- Type
- protein
- Length
- 240 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 14-3-3 protein sigma; Rap guanine nucleotide exchange factor 2
- UniProt
- P31947, Q9Y4G8
- Ligands
- NA, CA, CL
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 14-3-3 protein sigma | protein | 234 | 80% helix, 0% strand | P31947 |
| B | Rap guanine nucleotide exchange factor 2 | protein | 6 | 0% helix, 0% strand | Q9Y4G8 |
Ligands and binding sites
- NA · Sodium ion · metal · 5 copies · chains A
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 140 | 0.60 | 0.84 | 23 | empty |
| 2 | 61 | 0.30 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 447 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 6QDT · Crystal structure of 14-3-3sigma in complex with a RapGef2 pT740 phosphopeptide · the same entry in another collection · chain A against A, TM-score 1.00
- P31947 · AlphaFold monomer V2.0 prediction for 14-3-3 protein sigma (P31947) · a predicted model of the same protein · chain A against A, TM-score 0.95
- Q9Y4G8 · AlphaFold monomer V2.0 prediction for rap guanine nucleotide exchange factor 2 (Q9Y4G8) · a predicted model of the same protein · chain B against A, TM-score 0.63
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 P31947
- Every structure of UniProt Q9Y4G8
- Elsewhere: RCSB PDB 6QDT · PDBe 6QDT · UniProt P31947 · UniProt Q9Y4G8
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