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: 6R7I
Type: protein
Length: 3,739 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, Q9H9Q2, Q99627, Q13617, Q15370
Ligands: ZN
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 13 distinct chains · 56% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	COP9 signalosome complex subunit 1	protein	426	69% helix, 2% strand	Q13098
B	COP9 signalosome complex subunit 2	protein	428	66% helix, 1% strand	P61201
C	COP9 signalosome complex subunit 3	protein	400	56% helix, 1% strand	Q9UNS2
D	COP9 signalosome complex subunit 4	protein	407	71% helix, 2% strand	Q9BT78
E	COP9 signalosome complex subunit 5 (EC 3.4.-.-)	protein	298	46% helix, 12% strand	Q92905
F	COP9 signalosome complex subunit 6	protein	281	46% helix, 18% strand	Q7L5N1
G	COP9 signalosome complex subunit 7B	protein	215	60% helix, 3% strand	Q9H9Q2
H	COP9 signalosome complex subunit 8	protein	172	65% helix, 3% strand	Q99627
N	NEDD8	protein	78	23% helix, 27% strand	—
O	Cullin-2	protein	744	55% helix, 1% strand	Q13617
P	Elongin-B	protein	106	14% helix, 27% strand	Q15370
Q	Elongin-C	protein	99	38% helix, 15% strand	—
R	E3 ubiquitin-protein ligase RBX1	protein	85	15% helix, 0% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains E, N, R

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	1121	0.87	0.88	127	empty
2	1087	0.86	0.87	132	empty
3	635	0.86	0.90	95	empty
4	751	0.83	0.86	101	empty
5	453	0.82	0.89	72	empty

Interfaces

31 interfaces between chains.

E–F · 3796 Å² buried · 59 hydrogen bonds · protein-protein
O–R · 2214 Å² buried · 68 hydrogen bonds · protein-protein
A–C · 1798 Å² buried · 29 hydrogen bonds · protein-protein
F–G · 1356 Å² buried · 36 hydrogen bonds · protein-protein
P–Q · 1324 Å² buried · 30 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 isopeptide, 3 modified (isopeptide, engineered).

Compared structures

6R7I · Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome · the same entry in another collection · chain R against R, 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 Q9H9Q2
Every structure of UniProt Q99627
Every structure of UniProt Q13617
Every structure of UniProt Q15370
Elsewhere: RCSB PDB 6R7I · PDBe 6R7I · UniProt Q13098 · UniProt P61201 · UniProt Q9UNS2 · UniProt Q9BT78 · UniProt Q92905 · UniProt Q7L5N1 · UniProt Q9H9Q2 · UniProt Q99627 · UniProt Q13617 · UniProt Q15370

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