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Structure of the yeast heterotrimeric NUP82-NUP159-NUP116 nucleoporin complex

Analyse Structure of the yeast heterotrimeric NUP82-NUP159-NUP116 nucleoporin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3PBP
Type: protein
Length: 2,440 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoporin NUP82; Nucleoporin NUP116/NSP116; Nucleoporin NUP159
UniProt: P40368, Q02630, P40477
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 7 distinct chains · 20% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G	Nucleoporin NUP82	protein	438	16% helix, 38% strand	P40368
B, E, H, K	Nucleoporin NUP116/NSP116	protein	146	14% helix, 27% strand	Q02630
C, F	Nucleoporin NUP159	protein	26	73% helix, 0% strand	P40477
D	Nucleoporin NUP82	protein	437	16% helix, 38% strand	P40368
I	Nucleoporin NUP159	protein	28	82% helix, 0% strand	P40477
J	Nucleoporin NUP82	protein	439	18% helix, 38% strand	P40368
L	Nucleoporin NUP159	protein	24	83% helix, 0% strand	P40477

Ligands and binding sites

PGE · Triethylene glycol · additive · chains D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1156	0.80	0.81	104	empty
2	1150	0.77	0.79	78	empty
3	1161	0.77	0.79	78	empty
4	1141	0.76	0.78	76	empty
5	764	0.74	0.79	80	empty

Interfaces

15 interfaces between chains.

D–E · 1234 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1188 Å² buried · 26 hydrogen bonds · protein-protein
G–H · 1162 Å² buried · 27 hydrogen bonds · protein-protein
J–K · 1148 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 1069 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 39 modified (engineered).

Compared structures

3PBP · Structure of the yeast heterotrimeric Nup82-Nup159-Nup116 nucleoporin complex · 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 P40368
Every structure of UniProt Q02630
Every structure of UniProt P40477
Elsewhere: RCSB PDB 3PBP · PDBe 3PBP · UniProt P40368 · UniProt Q02630 · UniProt P40477

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