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Mercury activation of the plant aquaporin SOPIP2;1 - structural and functional characterization

Analyse Mercury activation of the plant aquaporin SOPIP2;1 - structural and functional… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4JC6
Type: protein
Length: 2,007 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aquaporin
UniProt: Q41372
Ligands: HG, CD
Pockets: 19 · best druggability 0.78

Structure

x-ray diffraction · 6 distinct chains · 69% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, H	Aquaporin	protein	252	68% helix, 4% strand	Q41372
C	Aquaporin	protein	249	69% helix, 4% strand	Q41372
D	Aquaporin	protein	251	69% helix, 4% strand	Q41372
J	Aquaporin	protein	251	69% helix, 4% strand	Q41372
L	Aquaporin	protein	250	69% helix, 4% strand	Q41372
N	Aquaporin	protein	250	70% helix, 4% strand	Q41372

Ligands and binding sites

HG · Mercury (II) ion · metal · 32 copies · chains A, D, C, B, H, N, L, J
CD · Cadmium ion · metal · 17 copies · chains A, B, C, D, H, J, L, N
BOG · octyl beta-D-glucopyranoside · additive · 13 copies · chains A, B, C, D, H, J, L, N

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

Pockets

19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	789	0.78	0.82	98	empty
2	908	0.77	0.80	96	empty
3	663	0.72	0.79	72	BOG
4	681	0.72	0.78	88	BOG
5	353	0.62	0.78	45	empty

Interfaces

20 interfaces between chains.

H–L · 1749 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 1746 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 1745 Å² buried · 9 hydrogen bonds · protein-protein
J–N · 1736 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 1727 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

4JC6 · Mercury activation of the plant aquaporin SoPIP2;1 - structural and functional… · the same entry in another collection · chain C against C, 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 Q41372
Elsewhere: RCSB PDB 4JC6 · PDBe 4JC6 · UniProt Q41372

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