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Crystal structure of heterochromatin protein SIR3 in complex with a silenced yeast nucleosome

Analyse Crystal structure of heterochromatin protein SIR3 in complex with a silenced… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4JJN
Type: protein + DNA
Length: 1,480 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3; Histone H4; Histone H2A.2; Histone H2B.2; Regulatory protein SIR3; DNA…
UniProt: P61830, P02309, P04912, P02294, P06701
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 12 distinct chains · 47% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3	protein	98	62% helix, 4% strand	P61830
B	Histone H4	protein	89	56% helix, 8% strand	P02309
C	Histone H2A.2	protein	105	53% helix, 7% strand	P04912
D	Histone H2B.2	protein	95	71% helix, 4% strand	P02294
E	Histone H3	protein	96	64% helix, 4% strand	P61830
F	Histone H4	protein	91	55% helix, 8% strand	P02309
G	Histone H2A.2	protein	106	53% helix, 7% strand	P04912
H	Histone H2B.2	protein	92	74% helix, 4% strand	P02294
K	Regulatory protein SIR3	protein	205	20% helix, 32% strand	P06701
L	Regulatory protein SIR3	protein	211	22% helix, 33% strand	P06701
I	DNA (146-mer)	dna	146	—	—
J	DNA (146-mer)	dna	146	—	—

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1150	0.78	0.80	100	empty
2	1044	0.78	0.80	78	empty
3	1026	0.78	0.80	82	empty
4	376	0.72	0.84	45	empty
5	510	0.72	0.81	59	empty

Interfaces

42 interfaces between chains.

I–J · 6703 Å² buried · 628 hydrogen bonds · nucleic-nucleic
E–F · 2681 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 2680 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 2608 Å² buried · 28 hydrogen bonds · protein-protein
G–H · 2527 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

4JJN · Crystal structure of heterochromatin protein Sir3 in complex with a silenced yeast… · the same entry in another collection · chain J against J, TM-score 1.00

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 P61830
Every structure of UniProt P02309
Every structure of UniProt P04912
Every structure of UniProt P02294
Every structure of UniProt P06701
Elsewhere: RCSB PDB 4JJN · PDBe 4JJN · UniProt P61830 · UniProt P02309 · UniProt P04912 · UniProt P02294 · UniProt P06701

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