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Crystal structure of CDYL2 in complex with H3K27ME3

Analyse Crystal structure of CDYL2 in complex with H3K27ME3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6V3N
Type: protein
Length: 149 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chromodomain Y-like protein 2; ACE-gln-leu-ala-thr-lys-ala-ala-arg-M3L-ser-ala-pro-ala…
UniProt: Q8N8U2
Ligands: UNX, NH2
Pockets: 2 · best druggability 0.38

Structure

x-ray diffraction · 4 distinct chains · 13% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chromodomain Y-like protein 2	protein	60	10% helix, 47% strand	Q8N8U2
B	Chromodomain Y-like protein 2	protein	62	21% helix, 44% strand	Q8N8U2
C	ACE-gln-leu-ala-thr-lys-ala-ala-arg-M3L-ser-ala-pro-ala- thr-tyr-NH2	protein	14	0% helix, 43% strand	—
D	ACE-gln-leu-ala-thr-lys-ala-ala-arg-M3L-ser-ala-pro-ala- thr-tyr-NH2	protein	13	0% helix, 38% strand	—

Ligands and binding sites

UNX · Unknown atom or ion · ion · 12 copies · chains A, C, B
NH2 · Amino group · ion · 2 copies · chains A, C, B, D

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	84	0.38	0.76	19	UNX
2	51	0.36	0.79	13	empty

Interfaces

4 interfaces between chains.

A–C · 873 Å² buried · 18 hydrogen bonds · protein-protein
B–D · 871 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 624 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 19 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (methylation).

Compared structures

6V3N · Crystal structure of CDYL2 in complex with H3K27me3 · the same entry in another collection · chain A against A, TM-score 1.00
Q8N8U2 · AlphaFold monomer V2.0 prediction for chromodomain Y-like protein 2 (Q8N8U2) · a predicted model of the same protein · chain A against A, TM-score 0.67

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 Q8N8U2
Elsewhere: RCSB PDB 6V3N · PDBe 6V3N · UniProt Q8N8U2

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