Research workbench

Structural basis of cullin-2 ring E3 ligase regulation by the COP9 signalosome

Analyse Structural basis of cullin-2 ring E3 ligase regulation by the COP9 signalosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6R6H
Type: protein
Length: 3,806 residues
Chains: 13
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: COP9 signalosome complex subunit 1; COP9 signalosome complex subunit 2; COP9 signalosome…
EC: 3.4.-.-
UniProt: Q13098, P61201, Q9UNS2, Q9BT78, Q92905, Q7L5N1, Q99627, Q13617, Q15370, P40337, Q9H9Q2
Ligands: ZN
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 13 distinct chains · 57% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	COP9 signalosome complex subunit 1	protein	419	69% helix, 1% strand	Q13098
B	COP9 signalosome complex subunit 2	protein	428	66% helix, 1% strand	P61201
C	COP9 signalosome complex subunit 3	protein	400	60% helix, 1% strand	Q9UNS2
D	COP9 signalosome complex subunit 4	protein	405	68% helix, 2% strand	Q9BT78
E	COP9 signalosome complex subunit 5 (EC 3.4.-.-)	protein	310	44% helix, 11% strand	Q92905
F	COP9 signalosome complex subunit 6	protein	281	44% helix, 18% strand	Q7L5N1
H	COP9 signalosome complex subunit 8	protein	172	67% helix, 3% strand	Q99627
O	Cullin-2	protein	745	61% helix, 2% strand	Q13617
P	Elongin-B	protein	105	4% helix, 11% strand	Q15370
Q	ELOC_HUMAN	protein	99	46% helix, 16% strand	—
R	RBX1_HUMAN	protein	86	19% helix, 3% strand	—
V	Von hippel-lindau disease tumor suppressor	protein	150	23% helix, 22% strand	P40337
G	COP9 signalosome complex subunit 7B	protein	206	66% helix, 2% strand	Q9H9Q2

Ligands and binding sites

ZN · Zinc ion · metal · chains E

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	446	0.82	0.89	71	empty
2	449	0.81	0.89	64	empty
3	1006	0.81	0.82	129	empty
4	1195	0.79	0.81	136	empty
5	963	0.78	0.81	114	empty

Interfaces

32 interfaces between chains.

E–F · 3923 Å² buried · 102 hydrogen bonds · protein-protein
O–R · 2083 Å² buried · 131 hydrogen bonds · protein-protein
A–C · 1902 Å² buried · 28 hydrogen bonds · protein-protein
D–F · 1478 Å² buried · 13 hydrogen bonds · protein-protein
F–G · 1441 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 isopeptide (isopeptide).

Compared structures

6R6H · Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome · the same entry in another collection · chain G against G, 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 Q13098
Every structure of UniProt P61201
Every structure of UniProt Q9UNS2
Every structure of UniProt Q9BT78
Every structure of UniProt Q92905
Every structure of UniProt Q7L5N1
Every structure of UniProt Q99627
Every structure of UniProt Q13617
Every structure of UniProt Q15370
Every structure of UniProt P40337
Every structure of UniProt Q9H9Q2
Elsewhere: RCSB PDB 6R6H · PDBe 6R6H · UniProt Q13098 · UniProt P61201 · UniProt Q9UNS2 · UniProt Q9BT78 · UniProt Q92905 · UniProt Q7L5N1 · UniProt Q99627 · UniProt Q13617 · UniProt Q15370 · UniProt P40337 · UniProt Q9H9Q2

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