MolNFT v1 · #183303 · protein

OSNIP2;1 silicon transporter from rice

7NL4 · Aquaporin NIP2-1: “OSNIP2;1 silicon transporter from rice”. X-ray diffraction, 1 ligand (CD), 20 pockets (best druggability 0.89). MolNFT v1 #183303 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7NL4
Type: protein
Length: 1,726 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aquaporin NIP2-1
UniProt: Q6Z2T3
Ligands: CD
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 2 distinct chains · 69% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, E, F, G, H	Aquaporin NIP2-1	protein	216	69% helix, 0% strand	Q6Z2T3
C	Aquaporin NIP2-1	protein	214	69% helix, 0% strand	Q6Z2T3

Ligands and binding sites

CD · Cadmium ion · metal · 9 copies · chains A, H, B, G, C, F, D, E

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	686	0.89	0.93	44	empty
2	752	0.89	0.92	48	empty
3	99	0.76	0.96	26	empty
4	338	0.75	0.86	53	empty
5	367	0.72	0.84	54	empty

Interfaces

20 interfaces between chains.

B–D · 1669 Å² buried · 7 hydrogen bonds · protein-protein
E–G · 1648 Å² buried · 7 hydrogen bonds · protein-protein
F–G · 1644 Å² buried · 14 hydrogen bonds · protein-protein
E–H · 1643 Å² buried · 13 hydrogen bonds · protein-protein
F–H · 1641 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

7NL4 · OsNIP2;1 silicon transporter from rice · the same entry in another collection · chain F against F, TM-score 1.00
Q6Z2T3 · AlphaFold monomer V2.0 prediction for aquaporin NIP2-1 (Q6Z2T3) · a predicted model of the same protein · chain C 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 Q6Z2T3
Elsewhere: RCSB PDB 7NL4 · PDBe 7NL4 · UniProt Q6Z2T3

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