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: 6R7F
Type: protein
Length: 3,931 residues
Chains: 14
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, Q9H9Q2, P40337, Q15370, Q15369, Q13617, Q15843
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · 14 distinct chains · 57% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	COP9 signalosome complex subunit 1	protein	433	65% helix, 3% strand	Q13098
B	COP9 signalosome complex subunit 2	protein	414	69% helix, 2% strand	P61201
C	COP9 signalosome complex subunit 3	protein	403	64% helix, 4% strand	Q9UNS2
D	COP9 signalosome complex subunit 4	protein	406	73% helix, 2% strand	Q9BT78
E	COP9 signalosome complex subunit 5 (EC 3.4.-.-)	protein	311	47% helix, 15% strand	Q92905
F	COP9 signalosome complex subunit 6	protein	288	47% helix, 22% strand	Q7L5N1
H	COP9 signalosome complex subunit 8	protein	168	72% helix, 7% strand	Q99627
G	COP9 signalosome complex subunit 7B	protein	208	66% helix, 7% strand	Q9H9Q2
V	Von hippel-lindau disease tumor suppressor	protein	160	24% helix, 28% strand	P40337
P	Elongin-B	protein	118	14% helix, 25% strand	Q15370
Q	Elongin-C	protein	112	38% helix, 11% strand	Q15369
O	Cullin-2	protein	744	63% helix, 4% strand	Q13617
R	E3 ubiquitin-protein ligase RBX1	protein	90	18% helix, 11% strand	—
N	NEDD8	protein	76	14% helix, 30% strand	Q15843

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	1176	0.81	0.82	109	empty
2	206	0.77	0.91	31	empty
3	572	0.73	0.81	72	empty
4	71	0.73	0.97	19	empty
5	745	0.73	0.79	76	empty

Interfaces

36 interfaces between chains.

E–F · 4562 Å² buried · 32 hydrogen bonds · protein-protein
A–C · 2310 Å² buried · 23 hydrogen bonds · protein-protein
O–R · 2189 Å² buried · 29 hydrogen bonds · protein-protein
F–G · 1966 Å² buried · 9 hydrogen bonds · protein-protein
C–H · 1869 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 isopeptide (isopeptide).

Compared structures

6R7F · Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome · the same entry in another collection · chain P against P, 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 Q9H9Q2
Every structure of UniProt P40337
Every structure of UniProt Q15370
Every structure of UniProt Q15369
Every structure of UniProt Q13617
Every structure of UniProt Q15843
Elsewhere: RCSB PDB 6R7F · PDBe 6R7F · UniProt Q13098 · UniProt P61201 · UniProt Q9UNS2 · UniProt Q9BT78 · UniProt Q92905 · UniProt Q7L5N1 · UniProt Q99627 · UniProt Q9H9Q2 · UniProt P40337 · UniProt Q15370 · UniProt Q15369 · UniProt Q13617 · UniProt Q15843

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.