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3.5 a cryo-EM structure of human uromodulin filament core

Analyse 3.5 a cryo-EM structure of human uromodulin filament core in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ZS5
Type: protein
Length: 257 residues
Chains: 2
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uromodulin
UniProt: P07911
Ligands: NAG, MAN, BMA
Pockets: 2 · best druggability 0.44

Structure

electron microscopy · 2 distinct chains · 0% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Uromodulin	protein	116	0% helix, 49% strand	P07911
D	Uromodulin	protein	141	0% helix, 41% strand	P07911

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, D
MAN · alpha-D-mannopyranose · sugar · 2 copies · chains D
BMA · beta-D-mannopyranose · sugar

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	79	0.44	0.80	21	empty
2	100	0.40	0.77	24	empty

Interfaces

1 interface between chains.

A–D · 2069 Å² buried · 29 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

6ZS5 · 3.5 A cryo-EM structure of human uromodulin filament core · the same entry in another collection · chain A against A, TM-score 1.00
P07911 · AlphaFold monomer V2.0 prediction for uromodulin (P07911) · a predicted model of the same protein · chain D against A, TM-score 0.88

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 P07911
Elsewhere: RCSB PDB 6ZS5 · PDBe 6ZS5 · UniProt P07911

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