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Crystal structure of dpy-30 DIMERIZATION/DOCKING domain in complex with ASH2L SDC1-dpy-30 interacting region (sdi)

Analyse Crystal structure of dpy-30 DIMERIZATION/DOCKING domain in complex with ASH2L… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4RIQ
Type: protein
Length: 974 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein dpy-30 homolog; SET1/ASH2 histone methyltransferase complex subunit ASH2
UniProt: Q9C005, Q9UBL3
Ligands: SO4
Pockets: 8 · best druggability 0.72

Structure

x-ray diffraction · 12 distinct chains · 77% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein dpy-30 homolog	protein	49	78% helix, 0% strand	Q9C005
B	Protein dpy-30 homolog	protein	47	79% helix, 0% strand	Q9C005
C, F, I, L, O, R, X	SET1/ASH2 histone methyltransferase complex subunit ASH2	protein	24	83% helix, 0% strand	Q9UBL3
D	Protein dpy-30 homolog	protein	51	80% helix, 0% strand	Q9C005
E, K	Protein dpy-30 homolog	protein	50	80% helix, 0% strand	Q9C005
G, M	Protein dpy-30 homolog	protein	50	74% helix, 0% strand	Q9C005
H	Protein dpy-30 homolog	protein	51	73% helix, 0% strand	Q9C005
J, Q, T, V	Protein dpy-30 homolog	protein	49	76% helix, 0% strand	Q9C005
N, S	Protein dpy-30 homolog	protein	48	77% helix, 0% strand	Q9C005
P	Protein dpy-30 homolog	protein	45	82% helix, 0% strand	Q9C005
U	SET1/ASH2 histone methyltransferase complex subunit ASH2	protein	23	83% helix, 0% strand	Q9UBL3
Z	Protein dpy-30 homolog	protein	48	71% helix, 0% strand	Q9C005

Ligands and binding sites

SO4 · Sulfate ion · ion · 8 copies · chains C, L, F, I, K, X, Z, O, U, R, Q

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	881	0.72	0.76	69	SO4
2	962	0.71	0.76	67	SO4
3	348	0.60	0.77	30	empty
4	362	0.59	0.76	39	empty
5	299	0.57	0.77	35	empty

Interfaces

58 interfaces between chains.

G–H · 1174 Å² buried · 12 hydrogen bonds · protein-protein
D–E · 1159 Å² buried · 12 hydrogen bonds · protein-protein
V–Z · 1106 Å² buried · 10 hydrogen bonds · protein-protein
J–K · 1101 Å² buried · 11 hydrogen bonds · protein-protein
M–N · 1094 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4RIQ · Crystal structure of DPY-30 dimerization/docking domain in complex with Ash2L Sdc1-DPY-30… · 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 Q9C005
Every structure of UniProt Q9UBL3
Elsewhere: RCSB PDB 4RIQ · PDBe 4RIQ · UniProt Q9C005 · UniProt Q9UBL3

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