MolNFT v1 · #124624 · protein

Structure of CTPRC2 in complex with H3K27ME3 and H3K27M

5KKL · Putative polycomb protein eed: “Structure of CTPRC2 in complex with H3K27ME3 and H3K27M”. X-ray diffraction, 2 ligands (SAM, ZN), 20 pockets (best druggability 0.87). MolNFT v1 #124624 on GenesisL1: 3D structure, binding sites and…

PDB: 5KKL
Type: protein
Length: 1,328 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative polycomb protein eed; Putative uncharacterized PROTEIN,HISTONE H3.1 PEPTIDE,ZINC…
UniProt: G0S8H7, G0SDW4, P68431, G0RYC6
Ligands: SAM, ZN
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 3 distinct chains · 27% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative polycomb protein eed	protein	481	10% helix, 39% strand	G0S8H7
B	Putative uncharacterized PROTEIN,HISTONE H3.1 PEPTIDE,ZINC finger domain-containing protein	protein	839	37% helix, 12% strand	G0SDW4, P68431, G0RYC6
D	Ala-ala-arg-M3L-ser-ala-pro-ala	protein	8	0% helix, 13% strand	—

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · chains B
ZN · Zinc ion · metal · 8 copies · chains B

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	917	0.87	0.89	93	empty
2	839	0.85	0.87	71	empty
3	481	0.82	0.89	63	empty
4	515	0.78	0.85	75	empty
5	742	0.73	0.79	76	SAM

Interfaces

3 interfaces between chains.

A–B · 5684 Å² buried · 66 hydrogen bonds · protein-protein
A–D · 503 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 194 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (methylation).

Compared structures

5KKL · Structure of ctPRC2 in complex with H3K27me3 and H3K27M · the same entry in another collection · chain D against D, TM-score 1.00
P68431 · AlphaFold monomer V2.0 prediction for histone H3.1 (P68431) · a predicted model of the same protein · chain B against A, TM-score 0.08

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 G0S8H7
Every structure of UniProt G0SDW4
Every structure of UniProt P68431
Every structure of UniProt G0RYC6
Elsewhere: RCSB PDB 5KKL · PDBe 5KKL · UniProt G0S8H7 · UniProt G0SDW4 · UniProt P68431 · UniProt G0RYC6

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.