MolNFT v1 · #93675 · protein

Complex structure 6 of DAXX/H3.3(SUB7)/H4

4H9S · Histone H3.3: “Complex structure 6 of DAXX/H3.3(SUB7)/H4”. X-ray diffraction, 1 ligand (PO4), 12 pockets (best druggability 0.88). MolNFT v1 #93675 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4H9S
Type: protein
Length: 733 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.3; Histone H4; Death domain-associated protein 6
UniProt: P84243, P62805, Q9UER7
Ligands: PO4
Pockets: 12 · best druggability 0.88

Structure

x-ray diffraction · 5 distinct chains · 69% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.3	protein	89	69% helix, 4% strand	P84243
B	Histone H3.3	protein	94	64% helix, 4% strand	P84243
C, D	Histone H4	protein	74	66% helix, 4% strand	P62805
E	Death domain-associated protein 6	protein	199	72% helix, 1% strand	Q9UER7
F	Death domain-associated protein 6	protein	203	71% helix, 1% strand	Q9UER7

Ligands and binding sites

PO4 · Phosphate ion · ion · 5 copies · chains A, C, B, D, E, F

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

Pockets

12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	960	0.88	0.89	92	empty
2	53	0.72	0.99	23	empty
3	260	0.71	0.86	31	empty
4	218	0.70	0.87	33	empty
5	445	0.69	0.80	44	PO4

Interfaces

14 interfaces between chains.

B–E · 2842 Å² buried · 35 hydrogen bonds · protein-protein
A–F · 2814 Å² buried · 38 hydrogen bonds · protein-protein
A–C · 1952 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 1888 Å² buried · 12 hydrogen bonds · protein-protein
C–F · 1613 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

4H9S · Complex structure 6 of DAXX/H3.3(sub7)/H4 · the same entry in another collection · chain F against F, TM-score 1.00
Q9UER7 · AlphaFold monomer V2.0 prediction for death domain-associated protein 6 (Q9UER7) · a predicted model of the same protein · chain F against A, TM-score 0.95
P84243 · AlphaFold monomer V2.0 prediction for histone H3.3 (P84243) · a predicted model of the same protein · chain A against A, TM-score 0.71

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 P84243
Every structure of UniProt P62805
Every structure of UniProt Q9UER7
Elsewhere: RCSB PDB 4H9S · PDBe 4H9S · UniProt P84243 · UniProt P62805 · UniProt Q9UER7

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