MolNFT v1 · #63237 · protein

Crystal structure of the nucleoporin pair NUP85-SEH1, space group P21212

3F3P · Nucleoporin SEH1: “Crystal structure of the nucleoporin pair NUP85-SEH1, space group P21212”. X-ray diffraction, 20 pockets (best druggability 0.88). MolNFT v1 #63237 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3F3P
Type: protein
Length: 4,728 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoporin SEH1; Nucleoporin NUP85
UniProt: P53011, P46673
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 9 distinct chains · 46% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, E	Nucleoporin SEH1	protein	303	2% helix, 52% strand	P53011
C	Nucleoporin NUP85	protein	480	61% helix, 5% strand	P46673
D	Nucleoporin NUP85	protein	478	61% helix, 5% strand	P46673
F, J	Nucleoporin SEH1	protein	308	2% helix, 51% strand	P53011
G	Nucleoporin NUP85	protein	483	60% helix, 4% strand	P46673
H	Nucleoporin NUP85	protein	486	60% helix, 4% strand	P46673
I	Nucleoporin SEH1	protein	307	2% helix, 51% strand	P53011
K	Nucleoporin NUP85	protein	487	60% helix, 4% strand	P46673
L	Nucleoporin NUP85	protein	482	60% helix, 5% strand	P46673

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	985	0.88	0.90	77	empty
2	1029	0.88	0.89	79	empty
3	1028	0.88	0.89	81	empty
4	1017	0.88	0.89	74	empty
5	1048	0.88	0.89	81	empty

Interfaces

17 interfaces between chains.

B–D · 3679 Å² buried · 40 hydrogen bonds · protein-protein
F–H · 3637 Å² buried · 38 hydrogen bonds · protein-protein
E–G · 3599 Å² buried · 36 hydrogen bonds · protein-protein
I–K · 3586 Å² buried · 42 hydrogen bonds · protein-protein
A–C · 3537 Å² buried · 44 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 97 modified (engineered).

Compared structures

3F3P · Crystal structure of the nucleoporin pair Nup85-Seh1, space group P21212 · 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 P53011
Every structure of UniProt P46673
Elsewhere: RCSB PDB 3F3P · PDBe 3F3P · UniProt P53011 · UniProt P46673

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