MolNFT v1 · #167238 · protein + DNA

Yeast compass in complex with a ubiquitinated nucleosome

6VEN · Histone H3.2: “Yeast compass in complex with a ubiquitinated nucleosome”. Electron microscopy, 2 ligands (SAM, ZN), 20 pockets (best druggability 0.84). MolNFT v1 #167238 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6VEN
Type: protein + DNA
Length: 2,563 residues
Chains: 18
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.2; Histone H4; Histone H2A type 1; Histone H2B 1.1; 601 DNA (146-mer)…
EC: 2.1.1.354
UniProt: P84233, P62799, P06897, P02281, P0CG48, P38123, P39706, P38827, P43132, Q03323, Q03012
Ligands: SAM, ZN
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 18 distinct chains · 32% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.2	protein	106	59% helix, 3% strand	P84233
B	Histone H4	protein	81	60% helix, 4% strand	P62799
C	Histone H2A type 1	protein	103	51% helix, 6% strand	P06897
D	Histone H2B 1.1	protein	93	73% helix, 4% strand	P02281
E	Histone H3.2	protein	97	66% helix, 1% strand	P84233
F	Histone H4	protein	80	61% helix, 4% strand	P62799
G	Histone H2A type 1	protein	106	47% helix, 4% strand	P06897
H	Histone H2B 1.1	protein	94	70% helix, 3% strand	P02281
I	601 DNA (146-mer)	dna	146	—	—
J	601 DNA (146-mer)	dna	146	—	—
K	Ubiquitin	protein	75	20% helix, 29% strand	P0CG48
L	Compass component SWD3	protein	308	2% helix, 46% strand	P38123
M	Compass component SWD1	protein	395	1% helix, 37% strand	P39706
N	Histone-lysine N-methyltransferase, H3 lysine-4 specific (EC 2.1.1.354)	protein	218	27% helix, 24% strand	P38827
O	Compass component BRE2	protein	315	17% helix, 32% strand	P43132
P	Compass component SDC1	protein	42	79% helix, 0% strand	Q03323
Q	Compass component SDC1	protein	29	72% helix, 0% strand	Q03323
R	Compass component SPP1	protein	129	62% helix, 0% strand	Q03012

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · chains N
ZN · Zinc ion · metal · chains N

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1076	0.84	0.85	115	empty
2	885	0.83	0.85	86	empty
3	660	0.80	0.84	77	empty
4	593	0.80	0.85	58	empty
5	1107	0.79	0.81	67	empty

Interfaces

57 interfaces between chains.

I–J · 6588 Å² buried · 497 hydrogen bonds · nucleic-nucleic
G–H · 2622 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 2612 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 2593 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 2585 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 modified (nonstandard).

Compared structures

6VEN · Yeast COMPASS in complex with a ubiquitinated nucleosome · 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 P84233
Every structure of UniProt P62799
Every structure of UniProt P06897
Every structure of UniProt P02281
Every structure of UniProt P0CG48
Every structure of UniProt P38123
Every structure of UniProt P39706
Every structure of UniProt P38827
Every structure of UniProt P43132
Every structure of UniProt Q03323
Every structure of UniProt Q03012
Elsewhere: RCSB PDB 6VEN · PDBe 6VEN · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt P02281 · UniProt P0CG48 · UniProt P38123 · UniProt P39706 · UniProt P38827 · UniProt P43132 · UniProt Q03323 · UniProt Q03012

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