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Crystal Structure of the UT-B Urea Transporter from Bos Taurus Bound to Selenourea
Analyse Crystal Structure of the UT-B Urea Transporter from Bos Taurus Bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EZD
- Type
- protein
- Length
- 1,037 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Bos taurus
- Molecule
- Urea transporter 1
- UniProt
- Q5QF96
- Ligands
- SEY, SPL, BGC
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.5 · 2 distinct chains · 69% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Urea transporter 1 | protein | 345 | 69% helix, 1% strand | Q5QF96 |
| B, C | Urea transporter 1 | protein | 346 | 69% helix, 1% strand | Q5QF96 |
Ligands and binding sites
- SEY · selenourea · ligand · 6 copies · chains A, B, C
- SPL · Octanoic acid (2-hydroxy-1-hydroxymethyl-heptadec-3-enyl)-amide · ligand · 3 copies · chains A, C, B
- BGC · beta-D-glucopyranose · sugar · 8 copies · chains A, B, C
- BOG · octyl beta-D-glucopyranoside · additive · 10 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.82 | 0.83 | 120 | SEY |
| 2 | 1183 | 0.79 | 0.79 | 87 | SPL |
| 3 | 423 | 0.68 | 0.80 | 54 | SEY |
| 4 | 485 | 0.68 | 0.79 | 65 | SEY |
| 5 | 379 | 0.68 | 0.80 | 44 | SEY |
Interfaces
3 interfaces between chains.
- B–C · 1224 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1209 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1202 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4EZD · Crystal structure of the ut-B urea transporter from bos taurus bound to selenourea · the same entry in another collection · chain A against A, TM-score 1.00
- Q5QF96 · AlphaFold monomer V2.0 prediction for urea transporter 1 (Q5QF96) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q5QF96
- Elsewhere: RCSB PDB 4EZD · PDBe 4EZD · UniProt Q5QF96
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