MolNFT v1 · #145214 · protein

Crystal structure of the yeast compass catalytic module

6CHG · KLLA0E24487P: “Crystal structure of the yeast compass catalytic module”. X-ray diffraction, 2 ligands (SAM, ZN), 13 pockets (best druggability 0.81). MolNFT v1 #145214 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6CHG
Type: protein
Length: 1,326 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: KLLA0E24487P; KLLA0C10945P; Histone-lysine N-methyltransferase, H3 lysine-4 specific…
EC: 2.1.1.43
UniProt: Q6CLY5, Q6CTQ1, Q6CIT4, Q6CXF3, Q6CPN6
Ligands: SAM, ZN
Pockets: 13 · best druggability 0.81

Structure

x-ray diffraction · 7 distinct chains · 12% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	KLLA0E24487P	protein	305	0% helix, 48% strand	Q6CLY5
B	KLLA0C10945P	protein	382	15% helix, 34% strand	Q6CTQ1
C	Histone-lysine N-methyltransferase, H3 lysine-4 specific (EC 2.1.1.43)	protein	143	16% helix, 38% strand	Q6CIT4
D	KLLA0A08800P	protein	408	3% helix, 42% strand	Q6CXF3
E	KLLA0E03521P	protein	42	79% helix, 0% strand	Q6CPN6
F	KLLA0E03521P	protein	43	70% helix, 0% strand	Q6CPN6
J	H3	protein	3	0% helix, 33% strand	—

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · chains C, J
ZN · Zinc ion · metal · chains C

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

Pockets

13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	826	0.81	0.84	69	empty
2	1144	0.80	0.82	118	empty
3	1185	0.79	0.81	73	empty
4	98	0.77	0.98	34	empty
5	286	0.72	0.85	39	SAM

Interfaces

9 interfaces between chains.

A–D · 2101 Å² buried · 21 hydrogen bonds · protein-protein
B–F · 1148 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 1117 Å² buried · 16 hydrogen bonds · protein-protein
E–F · 890 Å² buried · 4 hydrogen bonds · protein-protein
B–E · 649 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6CHG · Crystal structure of the yeast COMPASS catalytic module · the same entry in another collection · chain J against J, TM-score 1.00
Q6CIT4 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase, H3 lysine-4… · a predicted model of the same protein · chain C against A, TM-score 0.94

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 Q6CLY5
Every structure of UniProt Q6CTQ1
Every structure of UniProt Q6CIT4
Every structure of UniProt Q6CXF3
Every structure of UniProt Q6CPN6
Elsewhere: RCSB PDB 6CHG · PDBe 6CHG · UniProt Q6CLY5 · UniProt Q6CTQ1 · UniProt Q6CIT4 · UniProt Q6CXF3 · UniProt Q6CPN6

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