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Crystal structure of DNAJC9 hbd in complex with H3.3-H4 dimer and MCM2 hbd

Analyse Crystal structure of DNAJC9 hbd in complex with H3.3-H4 dimer and MCM2 hbd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7CJ0
Type: protein
Length: 590 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.3; Histone H4; DNA replication licensing factor MCM2; Dnaj homolog subfamily C…
EC: 3.6.4.12
UniProt: P84243, P62805, P49736, Q8WXX5
Pockets: 7 · best druggability 0.62

Structure

x-ray diffraction · 8 distinct chains · 64% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Histone H3.3	protein	77	66% helix, 5% strand	P84243
F	Histone H4	protein	84	64% helix, 5% strand	P62805
G	DNA replication licensing factor MCM2 (EC 3.6.4.12)	protein	60	35% helix, 5% strand	P49736
D	Dnaj homolog subfamily C member 9	protein	77	87% helix, 0% strand	Q8WXX5
B	Histone H3.3	protein	77	68% helix, 6% strand	P84243
C	Histone H4	protein	79	68% helix, 4% strand	P62805
H	DNA replication licensing factor MCM2 (EC 3.6.4.12)	protein	59	31% helix, 7% strand	P49736
A	Dnaj homolog subfamily C member 9	protein	77	81% helix, 0% strand	Q8WXX5

Ligands and binding sites

GOL · Glycerol · additive · chains E, G

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

Pockets

7 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	216	0.62	0.82	32	empty
2	246	0.58	0.79	38	empty
3	108	0.47	0.79	29	empty
4	130	0.47	0.78	22	empty
5	123	0.45	0.78	19	empty

Interfaces

13 interfaces between chains.

E–F · 2319 Å² buried · 23 hydrogen bonds · protein-protein
B–C · 2192 Å² buried · 15 hydrogen bonds · protein-protein
C–H · 1366 Å² buried · 24 hydrogen bonds · protein-protein
F–G · 1235 Å² buried · 17 hydrogen bonds · protein-protein
E–D · 941 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

7CJ0 · Crystal structure of DNAJC9 HBD in complex with H3.3-H4 dimer and MCM2 HBD · the same entry in another collection · chain A against A, TM-score 1.00
P84243 · AlphaFold monomer V2.0 prediction for histone H3.3 (P84243) · a predicted model of the same protein · chain E against A, TM-score 0.95
P62805 · AlphaFold monomer V2.0 prediction for histone H4 (P62805) · a predicted model of the same protein · chain C against A, TM-score 0.90

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 P49736
Every structure of UniProt Q8WXX5
Elsewhere: RCSB PDB 7CJ0 · PDBe 7CJ0 · UniProt P84243 · UniProt P62805 · UniProt P49736 · UniProt Q8WXX5

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