MolNFT v1 · #155074 · protein + DNA

The classb rsc-nucleosome complex

6KW4 · Histone H3.2: “The classb rsc-nucleosome complex”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.86). MolNFT v1 #155074 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6KW4
Type: protein + DNA
Length: 5,193 residues
Chains: 28
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.2; Histone H4; Histone H2A; DNA 167; Actin-related protein 7; Regulator of TY1…
EC: 3.6.4.12
UniProt: P84233, P62799, Q6AZJ8, Q12406, P53330, P32832, P43609, Q03124, P25632, Q06168, Q07979, P32597, Q9URQ5, P38781, Q06639, Q02206, Q06488, A0A1L8G0X3, Q05123
Ligands: ZN
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 26 distinct chains · 45% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
N	Histone H3.2	protein	98	62% helix, 3% strand	P84233
B	Histone H4	protein	82	57% helix, 5% strand	P62799
O, S	Histone H2A	protein	107	46% helix, 4% strand	Q6AZJ8
Q	Histone H3.2	protein	95	64% helix, 3% strand	P84233
R	Histone H4	protein	87	53% helix, 5% strand	P62799
U	DNA 167	dna	156	—	—
W	DNA 167 (EC 3.6.4.12)	dna	156	—	—
f	Actin-related protein 7	protein	398	42% helix, 20% strand	Q12406
h	Regulator of TY1 transposition protein 102	protein	54	13% helix, 28% strand	P53330
F	Chromatin structure-remodeling complex subunit RSC7	protein	118	39% helix, 11% strand	P32832
H	Chromatin structure-remodeling complex protein RSC8	protein	393	50% helix, 7% strand	P43609
D	Chromatin structure-remodeling complex protein RSC8	protein	305	53% helix, 3% strand	P43609
M	Chromatin structure-remodeling complex subunit RSC9	protein	384	59% helix, 2% strand	Q03124
I	Chromatin structure-remodeling complex protein RSC6	protein	244	50% helix, 8% strand	P25632
G	Chromatin structure-remodeling complex subunit SFH1	protein	246	31% helix, 15% strand	Q06168
A	Chromatin structure-remodeling complex protein RSC58	protein	365	37% helix, 7% strand	Q07979
J	Nuclear protein STH1/NPS1 (EC 3.6.4.12)	protein	235	51% helix, 2% strand	P32597
E	High temperature lethal protein 1	protein	58	76% helix, 0% strand	Q9URQ5
C	Chromatin structure-remodeling complex protein RSC30	protein	33	64% helix, 12% strand	P38781
K	Chromatin structure-remodeling complex protein RSC3	protein	42	45% helix, 10% strand	Q06639
X	Chromatin structure-remodeling complex subunit RSC4	protein	147	7% helix, 39% strand	Q02206
L	Chromatin structure-remodeling complex subunit RSC2	protein	85	19% helix, 11% strand	Q06488
P, T	Histone H4	protein	93	73% helix, 4% strand	A0A1L8G0X3
g	Actin-like protein ARP9	protein	395	36% helix, 20% strand	Q05123
V	Nuclear protein STH1/NPS1 (EC 3.6.4.12)	protein	69	96% helix, 0% strand	P32597
Y	Nuclear protein STH1/NPS1 (EC 3.6.4.12)	protein	548	35% helix, 7% strand	P32597

Ligands and binding sites

ZN · Zinc ion · metal · chains H, L

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	1161	0.86	0.87	96	empty
2	747	0.85	0.89	83	empty
3	1098	0.85	0.86	120	empty
4	269	0.85	0.95	48	empty
5	1082	0.83	0.84	113	empty

Interfaces

90 interfaces between chains.

U–W · 8150 Å² buried · 1,111 hydrogen bonds · nucleic-nucleic
A–J · 4744 Å² buried · 58 hydrogen bonds · protein-protein
H–D · 3876 Å² buried · 29 hydrogen bonds · protein-protein
H–I · 2832 Å² buried · 34 hydrogen bonds · protein-protein
H–G · 2799 Å² buried · 31 hydrogen bonds · protein-protein

Compared structures

6KW4 · The ClassB RSC-Nucleosome Complex · the same entry in another collection · chain f against f, 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 Q6AZJ8
Every structure of UniProt Q12406
Every structure of UniProt P53330
Every structure of UniProt P32832
Every structure of UniProt P43609
Every structure of UniProt Q03124
Every structure of UniProt P25632
Every structure of UniProt Q06168
Every structure of UniProt Q07979
Every structure of UniProt P32597
Every structure of UniProt Q9URQ5
Every structure of UniProt P38781
Every structure of UniProt Q06639
Every structure of UniProt Q02206
Every structure of UniProt Q06488
Every structure of UniProt A0A1L8G0X3
Every structure of UniProt Q05123
Elsewhere: RCSB PDB 6KW4 · PDBe 6KW4 · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt Q12406 · UniProt P53330 · UniProt P32832 · UniProt P43609 · UniProt Q03124 · UniProt P25632 · UniProt Q06168 · UniProt Q07979 · UniProt P32597 · UniProt Q9URQ5 · UniProt P38781 · UniProt Q06639 · UniProt Q02206 · UniProt Q06488 · UniProt A0A1L8G0X3 · UniProt Q05123

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