MolNFT v1 · #165300 · protein
Cryo-EM of native human uromodulin (UMOD)/TAMM-horsfall protein (thp) filament.
6TQK: “Cryo-EM of native human uromodulin (UMOD)/TAMM-horsfall protein (thp) filament.”. Electron microscopy, 4 ligands (NAG, MAN, BMA), 6 pockets (best druggability 0.52). MolNFT v1 #165300 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6TQK
- Type
- protein
- Length
- 593 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uromodulin
- UniProt
- P07911
- Ligands
- NAG, MAN, BMA, GAL
- Pockets
- 6 · best druggability 0.52
Structure
electron microscopy · 3 distinct chains · 7% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uromodulin | protein | 296 | 7% helix, 46% strand | P07911 |
| B | Uromodulin | protein | 144 | 0% helix, 47% strand | P07911 |
| C | Uromodulin | protein | 153 | 13% helix, 46% strand | P07911 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains B, A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- GAL · beta-D-galactopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.52 | 0.82 | 27 | empty |
| 2 | 51 | 0.50 | 0.86 | 20 | empty |
| 3 | 115 | 0.41 | 0.76 | 23 | empty |
| 4 | 62 | 0.38 | 0.79 | 14 | empty |
| 5 | 71 | 0.37 | 0.77 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2188 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2140 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 651 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6TQK · Cryo-EM of native 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 6TQK · PDBe 6TQK · UniProt P07911
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