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Crystal structure of the ut-B urea transporter from bos taurus

Analyse Crystal structure of the ut-B urea transporter from bos taurus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4EZC
Type: protein
Length: 1,037 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Urea transporter 1
UniProt: Q5QF96
Ligands: SPL, BGC
Pockets: 10 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 70% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Urea transporter 1	protein	345	70% helix, 1% strand	Q5QF96
B, C	Urea transporter 1	protein	346	70% helix, 1% strand	Q5QF96

Ligands and binding sites

SPL · Octanoic acid (2-hydroxy-1-hydroxymethyl-heptadec-3-enyl)-amide · ligand · 3 copies · chains A, B, C
BGC · beta-D-glucopyranose · sugar · 8 copies · chains A, B, C
BOG · octyl beta-D-glucopyranoside · additive · 10 copies · chains A, C, B

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

Pockets

10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	951	0.82	0.83	124	empty
2	1184	0.79	0.79	86	SPL
3	422	0.72	0.82	65	empty
4	403	0.67	0.80	52	empty
5	455	0.67	0.79	56	empty

Interfaces

3 interfaces between chains.

B–C · 1234 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 1226 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1206 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

4EZC · Crystal Structure of the UT-B Urea Transporter from Bos Taurus · 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 4EZC · PDBe 4EZC · UniProt Q5QF96

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