Research workbench
Cryo-EM of elastase-treated human uromodulin (UMOD)/TAMM-horsfall protein (thp) filament
Analyse Cryo-EM of elastase-treated human uromodulin (UMOD)/TAMM-horsfall protein (thp)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TQL
- Type
- protein
- Length
- 587 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uromodulin
- UniProt
- P07911
- Ligands
- NAG, MAN, BMA, GAL
- Pockets
- 5 · best druggability 0.59
Structure
electron microscopy · 3 distinct chains · 7% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uromodulin | protein | 293 | 7% helix, 45% strand | P07911 |
| B | Uromodulin | protein | 141 | 0% helix, 48% strand | P07911 |
| C | Uromodulin | protein | 153 | 13% helix, 44% strand | P07911 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 4 copies
- BMA · beta-D-mannopyranose · sugar · 2 copies
- GAL · beta-D-galactopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.59 | 0.88 | 25 | empty |
| 2 | 113 | 0.54 | 0.82 | 31 | empty |
| 3 | 71 | 0.42 | 0.80 | 18 | empty |
| 4 | 58 | 0.42 | 0.82 | 14 | empty |
| 5 | 101 | 0.39 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2159 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2118 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 673 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6TQL · Cryo-EM of elastase-treated human uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament · 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 B against A, TM-score 0.87
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 6TQL · PDBe 6TQL · UniProt P07911
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