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Crystal structure of N-terminal acetylated SIR3 bah domain D205N mutant in complex with yeast nucleosome core particle

Analyse Crystal structure of N-terminal acetylated SIR3 bah domain D205N mutant in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4KUD
Type: protein + DNA
Length: 1,485 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.1; Nucloesome DNA; Regulatory protein…
UniProt: P61830, P02309, P04912, P02293, P06701
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 10 distinct chains · 55% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3	protein	96	65% helix, 4% strand	P61830
B	Histone H4	protein	88	58% helix, 8% strand	P02309
C	Histone H2A.2	protein	103	53% helix, 7% strand	P04912
D	Histone H2B.1	protein	93	76% helix, 4% strand	P02293
E	Histone H3	protein	98	63% helix, 4% strand	P61830
F	Histone H4	protein	90	57% helix, 8% strand	P02309
G	Histone H2A.2	protein	105	51% helix, 7% strand	P04912
H	Histone H2B.1	protein	94	74% helix, 4% strand	P02293
I, J	Nucloesome DNA	dna	146	—	—
K, L	Regulatory protein SIR3	protein	213	28% helix, 32% strand	P06701

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	1132	0.78	0.80	90	empty
2	532	0.77	0.85	46	empty
3	576	0.76	0.83	56	empty
4	581	0.75	0.82	54	empty
5	1158	0.74	0.77	81	empty

Interfaces

45 interfaces between chains.

I–J · 6525 Å² buried · 562 hydrogen bonds · nucleic-nucleic
E–F · 2658 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 2639 Å² buried · 34 hydrogen bonds · protein-protein
A–B · 2624 Å² buried · 27 hydrogen bonds · protein-protein
G–H · 2588 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (nonstandard).

Compared structures

4KUD · Crystal structure of N-terminal acetylated Sir3 BAH domain D205N mutant in complex with… · the same entry in another collection · chain L against L, 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 P02293
Every structure of UniProt P06701
Elsewhere: RCSB PDB 4KUD · PDBe 4KUD · UniProt P61830 · UniProt P02309 · UniProt P04912 · UniProt P02293 · UniProt P06701

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