Research workbench

Double nuclear outer ring from the isolated yeast npc

Analyse Double nuclear outer ring from the isolated yeast npc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7N84
Type: protein
Length: 10,313 residues
Chains: 17
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoporin NUP188; Unknown; Nucleoporin NUP120; Nucleoporin NUP85; Nucleoporin 145C…
UniProt: P52593, P35729, P46673, P49687, Q04491, P53011, P52891, P36161
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 13 distinct chains · 34% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	Nucleoporin NUP188	protein	1137	41% helix, 0% strand	P52593
Y, Z	Unknown	protein	63	97% helix, 0% strand	—
a, l	Nucleoporin NUP120	protein	1006	26% helix, 15% strand	P35729
b	Nucleoporin NUP85	protein	675	30% helix, 2% strand	P46673
c	Nucleoporin 145C	protein	559	42% helix, 3% strand	P49687
d, o	Protein transport protein SEC13	protein	274	0% helix, 47% strand	Q04491
e, p	Nucleoporin SEH1	protein	307	0% helix, 39% strand	P53011
f	Nucleoporin NUP84	protein	649	48% helix, 0% strand	P52891
g	Nucleoporin NUP133	protein	1062	27% helix, 10% strand	P36161
m	Nucleoporin NUP85	protein	670	32% helix, 2% strand	P46673
n	Nucleoporin 145C	protein	557	49% helix, 2% strand	P49687
q	Nucleoporin NUP84	protein	648	45% helix, 1% strand	P52891
r	Nucleoporin NUP133	protein	1056	34% helix, 14% strand	P36161

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	561	0.87	0.93	62	empty
2	410	0.87	0.96	39	empty
3	602	0.85	0.90	55	empty
4	736	0.83	0.86	57	empty
5	145	0.81	0.97	23	empty

Interfaces

27 interfaces between chains.

m–p · 4280 Å² buried · 45 hydrogen bonds · protein-protein
b–e · 4024 Å² buried · 38 hydrogen bonds · protein-protein
c–d · 3589 Å² buried · 36 hydrogen bonds · protein-protein
n–o · 3290 Å² buried · 26 hydrogen bonds · protein-protein
X–q · 3017 Å² buried · 38 hydrogen bonds · protein-protein

Compared structures

7N84 · Double nuclear outer ring from the isolated yeast NPC · the same entry in another collection · chain l against l, 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 P52593
Every structure of UniProt P35729
Every structure of UniProt P46673
Every structure of UniProt P49687
Every structure of UniProt Q04491
Every structure of UniProt P53011
Every structure of UniProt P52891
Every structure of UniProt P36161
Elsewhere: RCSB PDB 7N84 · PDBe 7N84 · UniProt P52593 · UniProt P35729 · UniProt P46673 · UniProt P49687 · UniProt Q04491 · UniProt P53011 · UniProt P52891 · UniProt P36161

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