Research workbench
Crystal structure of the polymerization region of human UROMODULIN/TAMM-horsfall protein
Analyse Crystal structure of the polymerization region of human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WRN
- Type
- protein
- Length
- 1,356 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic PROTEIN,UROMODULIN
- UniProt
- P0AEY0, P07911
- Ligands
- GLC, NAG, ZN
- Pockets
- 16 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltose-binding periplasmic PROTEIN,UROMODULIN | protein | 693 | 29% helix, 31% strand | P0AEY0, P07911 |
| B | Maltose-binding periplasmic PROTEIN,UROMODULIN | protein | 663 | 30% helix, 33% strand | P0AEY0, P07911 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 832 | 0.85 | 0.87 | 93 | GLC |
| 2 | 318 | 0.71 | 0.84 | 32 | GLC |
| 3 | 424 | 0.70 | 0.81 | 43 | empty |
| 4 | 292 | 0.65 | 0.81 | 40 | empty |
| 5 | 164 | 0.65 | 0.86 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 3509 Ų buried · 52 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4WRN · Crystal structure of the polymerization region of human uromodulin/Tamm-Horsfall protein · 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 A against A, TM-score 0.44
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 P0AEY0
- Every structure of UniProt P07911
- Elsewhere: RCSB PDB 4WRN · PDBe 4WRN · UniProt P0AEY0 · UniProt P07911
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