Research workbench

SPT16-H2A-H2B fact histone complex

Analyse SPT16-H2A-H2B fact histone complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4WNN
Type: protein
Length: 731 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H2A.1; Histone H2B.1; SPT16
UniProt: P04911, P02293
Ligands: PO4
Pockets: 4 · best druggability 0.68

Structure

x-ray diffraction · 6 distinct chains · 68% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H2A.1	protein	86	67% helix, 5% strand	P04911
B, F, H	Histone H2B.1	protein	98	70% helix, 4% strand	P02293
C, E	Histone H2A.1	protein	83	69% helix, 5% strand	P04911
D	Histone H2B.1	protein	97	71% helix, 5% strand	P02293
G	Histone H2A.1	protein	82	66% helix, 5% strand	P04911
T	SPT16	protein	6	0% helix, 17% strand	—

Ligands and binding sites

PO4 · Phosphate ion · ion · 2 copies · chains A, B, E, F

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	804	0.68	0.75	65	empty
2	821	0.67	0.74	62	empty
3	66	0.38	0.79	16	empty
4	53	0.29	0.76	10	empty

Interfaces

23 interfaces between chains.

G–H · 2543 Å² buried · 21 hydrogen bonds · protein-protein
E–F · 2516 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 2507 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 2493 Å² buried · 29 hydrogen bonds · protein-protein
F–H · 653 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

P04911 · AlphaFold monomer V2.0 prediction for histone H2A.1 (P04911) · a predicted model of the same protein · chain G against A, TM-score 0.97
P02293 · AlphaFold monomer V2.0 prediction for histone H2B.1 (P02293) · a predicted model of the same protein · chain D against A, TM-score 0.91

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 P04911
Every structure of UniProt P02293
Elsewhere: RCSB PDB 4WNN · PDBe 4WNN · UniProt P04911 · UniProt P02293

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