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Crystal structure of a SUZ12-RBBP4-PHF19-JARID2 heterotetrameric complex

Analyse Crystal structure of a SUZ12-RBBP4-PHF19-JARID2 heterotetrameric complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NQ3
Type: protein
Length: 1,470 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone-binding protein RBBP4; Polycomb protein SUZ12; Phd finger protein 19; Protein…
UniProt: Q09028, Q15022, Q5T6S3, Q92833
Ligands: ZN
Pockets: 19 · best druggability 0.83

Structure

x-ray diffraction · 7 distinct chains · 17% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone-binding protein RBBP4	protein	381	10% helix, 43% strand	Q09028
B	Polycomb protein SUZ12	protein	291	22% helix, 28% strand	Q15022
C	Phd finger protein 19	protein	53	38% helix, 32% strand	Q5T6S3
D, H	Protein jumonji	protein	17	59% helix, 6% strand	Q92833
E	Histone-binding protein RBBP4	protein	382	8% helix, 45% strand	Q09028
F	Polycomb protein SUZ12	protein	278	23% helix, 29% strand	Q15022
G	Phd finger protein 19	protein	51	37% helix, 22% strand	Q5T6S3

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains B, F

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

Pockets

19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1070	0.83	0.84	90	empty
2	405	0.75	0.85	31	empty
3	237	0.72	0.87	30	empty
4	426	0.71	0.82	53	empty
5	297	0.63	0.80	31	empty

Interfaces

12 interfaces between chains.

E–F · 4344 Å² buried · 86 hydrogen bonds · protein-protein
A–B · 4326 Å² buried · 84 hydrogen bonds · protein-protein
F–H · 925 Å² buried · 22 hydrogen bonds · protein-protein
B–D · 904 Å² buried · 26 hydrogen bonds · protein-protein
B–C · 883 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

6NQ3 · Crystal Structure of a SUZ12-RBBP4-PHF19-JARID2 Heterotetrameric Complex · the same entry in another collection · chain H against H, TM-score 1.00
Q09028 · AlphaFold monomer V2.0 prediction for histone-binding protein RBBP4 (Q09028) · a predicted model of the same protein · chain E against A, TM-score 0.99
Q5T6S3 · AlphaFold monomer V2.0 prediction for phd finger protein 19 (Q5T6S3) · a predicted model of the same protein · chain C against A, TM-score 0.64

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 Q09028
Every structure of UniProt Q15022
Every structure of UniProt Q5T6S3
Every structure of UniProt Q92833
Elsewhere: RCSB PDB 6NQ3 · PDBe 6NQ3 · UniProt Q09028 · UniProt Q15022 · UniProt Q5T6S3 · UniProt Q92833

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