Research workbench

Cryo EM structure of human seipin

Analyse Cryo EM structure of human seipin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6DS5
Type: protein
Length: 1,760 residues
Chains: 11
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Seipin
UniProt: Q96G97
Ligands: NAG
Pockets: 20 · best druggability 0.76

Structure

electron microscopy · 1 distinct chain · 14% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K	Seipin	protein	160	14% helix, 33% strand	Q96G97

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains A, B, C, D, E, F, G, H, I, J, K

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	108	0.76	0.95	25	empty
2	102	0.76	0.96	19	empty
3	103	0.76	0.96	19	empty
4	104	0.75	0.96	20	empty
5	103	0.75	0.95	19	empty

Interfaces

11 interfaces between chains.

C–D · 1155 Å² buried · 8 hydrogen bonds · protein-protein
G–H · 1155 Å² buried · 8 hydrogen bonds · protein-protein
D–E · 1154 Å² buried · 8 hydrogen bonds · protein-protein
H–I · 1151 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 1151 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 11 disulfide, 11 glycan (disulfide, N-glycosylation).

Compared structures

6DS5 · Cryo EM structure of human SEIPIN · the same entry in another collection · chain K against K, TM-score 1.00
Q96G97 · AlphaFold monomer V2.0 prediction for seipin (Q96G97) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 Q96G97
Elsewhere: RCSB PDB 6DS5 · PDBe 6DS5 · UniProt Q96G97

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