MolNFT v1 · #101011 · protein

X-ray structure of human aquaporin 2

4NEF · Aquaporin-2: “X-ray structure of human aquaporin 2”. X-ray diffraction, 2 ligands (CD, ZN), 8 pockets (best druggability 0.69). MolNFT v1 #101011 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4NEF
Type: protein
Length: 940 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aquaporin-2
UniProt: P41181
Ligands: CD, ZN
Pockets: 8 · best druggability 0.69

Structure

x-ray diffraction · 4 distinct chains · 71% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Aquaporin-2	protein	239	70% helix, 0% strand	P41181
B	Aquaporin-2	protein	233	73% helix, 0% strand	P41181
C	Aquaporin-2	protein	236	72% helix, 0% strand	P41181
D	Aquaporin-2	protein	232	71% helix, 0% strand	P41181

Ligands and binding sites

CD · Cadmium ion · metal · 2 copies · chains A, D
ZN · Zinc ion · metal · chains A

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

Pockets

8 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	461	0.69	0.80	63	empty
2	543	0.67	0.77	73	CD
3	401	0.64	0.78	46	empty
4	285	0.61	0.79	50	empty
5	320	0.60	0.78	51	ZN

Interfaces

6 interfaces between chains.

A–D · 1939 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 1842 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 1754 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 1716 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 115 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

4NEF · X-ray structure of human Aquaporin 2 · the same entry in another collection · chain D against D, TM-score 1.00
P41181 · AlphaFold monomer V2.0 prediction for aquaporin-2 (P41181) · a predicted model of the same protein · chain D against A, TM-score 0.95

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 P41181
Elsewhere: RCSB PDB 4NEF · PDBe 4NEF · UniProt P41181

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