Research workbench

26S proteasome wt-UBP6-ubvs complex in the si state (atpases, RPN1, UBP6, and ubvs)

Analyse 26S proteasome wt-UBP6-ubvs complex in the si state (atpases, RPN1, UBP6, and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7QO4
Type: protein
Length: 3,737 residues
Chains: 9
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 26S proteasome regulatory subunit RPN1; RPT1 isoform 1; RPT2 isoform 1; RPT3 isoform 1…
EC: 3.4.19.12
UniProt: P38764, A0A6A5PV22, A0A6A5Q382, A0A6A5PYF7, A0A6A5Q8D3, A0A6A5Q672, A0A6A5PWS2, A0A6A5PXS0, J3QS39
Ligands: ATP, ADP, MG
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 9 distinct chains · 43% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
Z	26S proteasome regulatory subunit RPN1	protein	906	60% helix, 2% strand	P38764
H	RPT1 isoform 1	protein	391	36% helix, 15% strand	A0A6A5PV22
I	RPT2 isoform 1	protein	384	34% helix, 16% strand	A0A6A5Q382
K	RPT3 isoform 1	protein	394	40% helix, 14% strand	A0A6A5PYF7
L	RPT4 isoform 1	protein	388	41% helix, 14% strand	A0A6A5Q8D3
M	RPT5 isoform 1	protein	421	41% helix, 13% strand	A0A6A5Q672
J	RPT6 isoform 1	protein	405	41% helix, 14% strand	A0A6A5PWS2
8	Ubiquitin carboxyl-terminal hydrolase (EC 3.4.19.12)	protein	372	34% helix, 26% strand	A0A6A5PXS0
9	Polyubiquitin-B	protein	76	20% helix, 34% strand	J3QS39

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 5 copies · chains H, I, J, K, L, M
ADP · Adenosine-5'-diphosphate · ligand · chains J
MG · Magnesium ion · metal · 6 copies · chains H, I, J, K, L, M

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	934	0.86	0.87	98	empty
2	210	0.82	0.96	29	empty
3	1051	0.82	0.83	101	ATP, MG
4	608	0.80	0.86	57	ATP, MG
5	844	0.80	0.83	94	empty

Interfaces

21 interfaces between chains.

L–M · 5643 Å² buried · 45 hydrogen bonds · protein-protein
H–I · 4515 Å² buried · 35 hydrogen bonds · protein-protein
K–J · 3510 Å² buried · 36 hydrogen bonds · protein-protein
K–L · 3089 Å² buried · 38 hydrogen bonds · protein-protein
H–M · 2997 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (nonstandard).

Compared structures

7QO4 · 26S proteasome WT-Ubp6-UbVS complex in the si state (ATPases, Rpn1, Ubp6, and UbVS) · the same entry in another collection · chain 9 against 9, TM-score 1.00
P38764 · AlphaFold monomer V2.0 prediction for 26S proteasome regulatory subunit RPN1 (P38764) · a predicted model of the same protein · chain Z against A, TM-score 0.83

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 P38764
Every structure of UniProt A0A6A5PV22
Every structure of UniProt A0A6A5Q382
Every structure of UniProt A0A6A5PYF7
Every structure of UniProt A0A6A5Q8D3
Every structure of UniProt A0A6A5Q672
Every structure of UniProt A0A6A5PWS2
Every structure of UniProt A0A6A5PXS0
Every structure of UniProt J3QS39
Elsewhere: RCSB PDB 7QO4 · PDBe 7QO4 · UniProt P38764 · UniProt A0A6A5PV22 · UniProt A0A6A5Q382 · UniProt A0A6A5PYF7 · UniProt A0A6A5Q8D3 · UniProt A0A6A5Q672 · UniProt A0A6A5PWS2 · UniProt A0A6A5PXS0 · UniProt J3QS39

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