Research workbench

Crystal structure of the full length S156E mutant of human aquaporin 5

Analyse Crystal structure of the full length S156E mutant of human aquaporin 5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5DYE
Type: protein
Length: 981 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aquaporin-5
UniProt: P55064
Ligands: PS6
Pockets: 13 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 68% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Aquaporin-5	protein	243	67% helix, 0% strand	P55064
B	Aquaporin-5	protein	243	69% helix, 0% strand	P55064
C	Aquaporin-5	protein	242	68% helix, 0% strand	P55064
D	Aquaporin-5	protein	253	66% helix, 0% strand	P55064

Ligands and binding sites

PS6 · O-[(S)-{[(2S)-2-(hexanoyloxy)-3-(tetradecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-D-serine · ligand · chains A, B, C, D

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

Pockets

13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	267	0.82	0.93	47	PS6
2	524	0.67	0.78	52	empty
3	409	0.65	0.79	54	empty
4	360	0.65	0.79	54	empty
5	332	0.59	0.77	45	empty

Interfaces

6 interfaces between chains.

A–D · 1691 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 1637 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 1609 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 1599 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 16 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5DYE · Crystal structure of the full length S156E mutant of human aquaporin 5 · the same entry in another collection · chain B against B, TM-score 1.00
P55064 · AlphaFold monomer V2.0 prediction for aquaporin-5 (P55064) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 P55064
Elsewhere: RCSB PDB 5DYE · PDBe 5DYE · UniProt P55064

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.