Research workbench

Human aquaporin 5 (AQP5) - high resolution X-ray structure

Analyse Human aquaporin 5 (AQP5) - high resolution X-ray structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3D9S
Type: protein
Length: 978 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aquaporin-5
UniProt: P55064
Ligands: PS6
Pockets: 12 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 68% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Aquaporin-5	protein	245	70% helix, 0% strand	P55064
C	Aquaporin-5	protein	243	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

12 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	235	0.79	0.91	36	PS6
2	473	0.69	0.79	61	empty
3	457	0.68	0.79	62	empty
4	405	0.67	0.79	54	empty
5	419	0.66	0.79	63	empty

Interfaces

5 interfaces between chains.

A–C · 1564 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 1553 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 1552 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 1544 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 18 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3D9S · Human Aquaporin 5 (AQP5) - High Resolution X-ray Structure · the same entry in another collection · chain C against C, 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 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 P55064
Elsewhere: RCSB PDB 3D9S · PDBe 3D9S · UniProt P55064

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