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Cryoem structure INO80CORE nucleosome complex

Analyse Cryoem structure INO80CORE nucleosome complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6FML
Type: protein + DNA
Length: 5,114 residues
Chains: 20
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ruvb-like helicase; INO80; LES2; IES6; Actin related protein 5; Nucleosomal DNA strand 1…
EC: 3.6.4.12
UniProt: G0RYI5, G0RYC2, G0RY01, G0S590, G0S589, Q71DI3, P62805, P0C0S9, P62807
Ligands: ADP, ATP
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 19 distinct chains · 40% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ruvb-like helicase (EC 3.6.4.12)	protein	449	35% helix, 20% strand	G0RYI5
B	Ruvb-like helicase (EC 3.6.4.12)	protein	438	36% helix, 21% strand	G0RYI5
C	Ruvb-like helicase (EC 3.6.4.12)	protein	459	33% helix, 21% strand	G0RYI5
D	Ruvb-like helicase (EC 3.6.4.12)	protein	439	34% helix, 23% strand	G0RYC2
E	Ruvb-like helicase (EC 3.6.4.12)	protein	441	36% helix, 21% strand	G0RYC2
F	Ruvb-like helicase (EC 3.6.4.12)	protein	437	37% helix, 24% strand	G0RYC2
G	INO80	protein	731	41% helix, 9% strand	—
H	LES2	protein	66	53% helix, 14% strand	G0RY01
I	IES6	protein	109	29% helix, 4% strand	G0S590
J	Actin related protein 5	protein	503	41% helix, 14% strand	G0S589
K	Nucleosomal DNA strand 1	dna	144	—	—
L	Nucleosomal DNA strand 2	dna	144	—	—
M	Histone H3.2	protein	95	64% helix, 4% strand	Q71DI3
N	Histone H4	protein	79	63% helix, 9% strand	P62805
O	Histone H2A type 1	protein	104	55% helix, 7% strand	P0C0S9
P, T	Histone H2B type 1-C/E/F/G/I	protein	95	71% helix, 4% strand	P62807
Q	Histone H3.2	protein	97	65% helix, 4% strand	Q71DI3
R	Histone H4	protein	82	62% helix, 9% strand	P62805
S	Histone H2A type 1	protein	107	52% helix, 7% strand	P0C0S9

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, D, B, E, C, F
ATP · Adenosine-5'-triphosphate · ligand · chains J

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	855	0.87	0.89	93	empty
2	965	0.85	0.87	95	empty
3	786	0.84	0.87	75	empty
4	308	0.84	0.94	45	ADP
5	253	0.83	0.95	37	ADP

Interfaces

78 interfaces between chains.

K–L · 6495 Å² buried · 542 hydrogen bonds · nucleic-nucleic
C–F · 4136 Å² buried · 40 hydrogen bonds · protein-protein
B–F · 4078 Å² buried · 34 hydrogen bonds · protein-protein
C–D · 3846 Å² buried · 34 hydrogen bonds · protein-protein
B–E · 3680 Å² buried · 35 hydrogen bonds · protein-protein

Compared structures

6FML · CryoEM Structure INO80core Nucleosome complex · the same entry in another collection · chain K against K, 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 G0RYI5
Every structure of UniProt G0RYC2
Every structure of UniProt G0RY01
Every structure of UniProt G0S590
Every structure of UniProt G0S589
Every structure of UniProt Q71DI3
Every structure of UniProt P62805
Every structure of UniProt P0C0S9
Every structure of UniProt P62807
Elsewhere: RCSB PDB 6FML · PDBe 6FML · UniProt G0RYI5 · UniProt G0RYC2 · UniProt G0RY01 · UniProt G0S590 · UniProt G0S589 · UniProt Q71DI3 · UniProt P62805 · UniProt P0C0S9 · UniProt P62807

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