MolNFT v1 · #171036 · protein

14-3-3 sigma in complex with HDM2-186 peptide

6YR6 · 14-3-3 protein sigma: “14-3-3 sigma in complex with HDM2-186 peptide”. X-ray diffraction, 1 ligand (IOD), 13 pockets (best druggability 0.64). MolNFT v1 #171036 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6YR6
Type: protein
Length: 940 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 14-3-3 protein sigma; HDM2-186
UniProt: P31947
Ligands: IOD
Pockets: 13 · best druggability 0.64

Structure

x-ray diffraction · 4 distinct chains · 80% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	14-3-3 protein sigma	protein	232	82% helix, 0% strand	P31947
B, D, F, H	HDM2-186	protein	6	0% helix, 0% strand	—
C, E	14-3-3 protein sigma	protein	229	80% helix, 0% strand	P31947
G	14-3-3 protein sigma	protein	226	81% helix, 0% strand	P31947

Ligands and binding sites

IOD · Iodide ion · ion · 11 copies · chains A, E, C, F, G
B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, C, E, G

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	586	0.64	0.75	37	IOD, B3P
2	481	0.60	0.74	35	IOD, B3P
3	163	0.55	0.80	22	empty
4	222	0.52	0.76	27	empty
5	140	0.48	0.78	18	empty

Interfaces

9 interfaces between chains.

A–E · 1009 Å² buried · 12 hydrogen bonds · protein-protein
G–H · 531 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 524 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 514 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 452 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

6YR6 · 14-3-3 sigma in complex with hDM2-186 peptide · the same entry in another collection · chain C against C, 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 E against A, TM-score 0.96

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
Elsewhere: RCSB PDB 6YR6 · PDBe 6YR6 · UniProt P31947

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