MolNFT v1 · #18283 · protein

Unbound form of tomato inhibitor-II

1PJU · Wound-induced proteinase inhibitor II: “Unbound form of tomato inhibitor-II”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.72). MolNFT v1 #18283 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1PJU
Type: protein
Length: 456 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Wound-induced proteinase inhibitor II
UniProt: P05119
Ligands: SO4
Pockets: 5 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 0% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Wound-induced proteinase inhibitor II	protein	115	0% helix, 26% strand	P05119
B	Wound-induced proteinase inhibitor II	protein	113	0% helix, 28% strand	P05119
C, D	Wound-induced proteinase inhibitor II	protein	114	0% helix, 26% strand	P05119

Ligands and binding sites

SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	528	0.72	0.80	44	empty
2	457	0.71	0.81	45	empty
3	81	0.54	0.85	20	empty
4	166	0.51	0.79	24	SO4
5	60	0.30	0.75	17	empty

Interfaces

3 interfaces between chains.

A–C · 974 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 970 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 614 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 disulfide (disulfide).

Compared structures

1PJU · Unbound form of Tomato Inhibitor-II · the same entry in another collection · chain D against D, TM-score 1.00
P05119 · AlphaFold monomer V2.0 prediction for wound-induced proteinase inhibitor 2 (P05119) · a predicted model of the same protein · chain A 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 P05119
Elsewhere: RCSB PDB 1PJU · PDBe 1PJU · UniProt P05119

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