MolNFT v1 · #114531 · protein

Structure of histone H3/H4 in complex with SPT2

5BSA · Histone H3.2: “Structure of histone H3/H4 in complex with SPT2”. X-ray diffraction, 6 pockets (best druggability 0.79). MolNFT v1 #114531 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5BSA
Type: protein
Length: 380 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.2; Histone H4; Protein SPT2 homolog
UniProt: P84233, P62799, Q68D10
Pockets: 6 · best druggability 0.79

Structure

x-ray diffraction · 6 distinct chains · 56% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.2	protein	75	68% helix, 4% strand	P84233
B	Histone H3.2	protein	76	62% helix, 5% strand	P84233
C	Histone H4	protein	69	59% helix, 4% strand	P62799
D	Histone H4	protein	68	66% helix, 6% strand	P62799
E	Protein SPT2 homolog	protein	69	30% helix, 1% strand	Q68D10
F	Protein SPT2 homolog	protein	23	30% helix, 0% strand	Q68D10

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	442	0.79	0.87	61	empty
2	468	0.74	0.83	61	empty
3	205	0.53	0.78	29	empty
4	180	0.47	0.76	22	empty
5	68	0.33	0.75	17	empty

Interfaces

10 interfaces between chains.

B–D · 1512 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 1469 Å² buried · 6 hydrogen bonds · protein-protein
C–E · 854 Å² buried · 14 hydrogen bonds · protein-protein
A–E · 689 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 535 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (engineered).

Compared structures

5BSA · Structure of histone H3/H4 in complex with Spt2 · the same entry in another collection · chain F against F, TM-score 1.00
Q68D10 · AlphaFold monomer V2.0 prediction for protein SPT2 homolog (Q68D10) · a predicted model of the same protein · chain E against A, TM-score 0.77

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 P84233
Every structure of UniProt P62799
Every structure of UniProt Q68D10
Elsewhere: RCSB PDB 5BSA · PDBe 5BSA · UniProt P84233 · UniProt P62799 · UniProt Q68D10

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