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Crystal structure of human GLE1 ctd-NUP42 gbm complex

Analyse Crystal structure of human GLE1 ctd-NUP42 gbm complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6B4F
Type: protein
Length: 718 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoporin GLE1; Nucleoporin like 2
UniProt: Q53GS7, Q3B7J4
Ligands: PO4, CL
Pockets: 11 · best druggability 0.64

Structure

x-ray diffraction · 3 distinct chains · 64% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Nucleoporin GLE1	protein	315	66% helix, 2% strand	Q53GS7
A	Nucleoporin GLE1	protein	313	68% helix, 2% strand	Q53GS7
C, D	Nucleoporin like 2	protein	45	24% helix, 0% strand	Q3B7J4

Ligands and binding sites

PO4 · Phosphate ion · ion · 2 copies · chains B, A
CL · Chloride ion · ion · 2 copies · chains A, D, B, C

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

Pockets

11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	428	0.64	0.77	53	empty
2	259	0.58	0.78	31	PO4
3	142	0.56	0.82	16	CL
4	127	0.53	0.81	16	CL
5	161	0.42	0.74	24	empty

Interfaces

5 interfaces between chains.

B–C · 1366 Å² buried · 24 hydrogen bonds · protein-protein
A–D · 1322 Å² buried · 13 hydrogen bonds · protein-protein
B–A · 958 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 67 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 57 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6B4F · Crystal structure of human Gle1 CTD-Nup42 GBM complex · the same entry in another collection · chain B against B, TM-score 1.00
Q53GS7 · AlphaFold monomer V2.0 prediction for nucleoporin GLE1 (Q53GS7) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 Q53GS7
Every structure of UniProt Q3B7J4
Elsewhere: RCSB PDB 6B4F · PDBe 6B4F · UniProt Q53GS7 · UniProt Q3B7J4

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