MolNFT v1 · #47541 · protein

Mechanism of auxin perception by the TIR1 ubiquitin ligase

2P1O · SKP1-like protein 1A: “Mechanism of auxin perception by the TIR1 ubiquitin ligase”. X-ray diffraction, 2 ligands (IHP, NLA), 4 pockets (best druggability 0.79). MolNFT v1 #47541 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 2P1O
Type: protein
Length: 711 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SKP1-like protein 1A; Transport inhibitor response 1 protein; Auxin-responsive protein…
UniProt: Q39255, Q570C0, Q38825
Ligands: IHP, NLA
Pockets: 4 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SKP1-like protein 1A	protein	127	59% helix, 8% strand	Q39255
B	Transport inhibitor response 1 protein	protein	571	37% helix, 19% strand	Q570C0
C	Auxin-responsive protein IAA7	protein	13	0% helix, 15% strand	Q38825

Ligands and binding sites

IHP · Inositol hexakisphosphate · ligand · chains B
NLA · Naphthalen-1-yl-acetic acid · ligand · chains B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	850	0.79	0.82	91	IHP, NLA
2	150	0.49	0.78	26	empty
3	56	0.44	0.84	17	empty
4	91	0.41	0.78	17	empty

Interfaces

2 interfaces between chains.

A–B · 1706 Å² buried · 22 hydrogen bonds · protein-protein
B–C · 753 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

2P1O · Mechanism of Auxin Perception by the TIR1 ubiquitin ligase · the same entry in another collection · chain A against A, TM-score 1.00
Q570C0 · AlphaFold monomer V2.0 prediction for protein transport inhibitor response 1 (Q570C0) · a predicted model of the same protein · chain B against A, TM-score 0.99
Q39255 · AlphaFold monomer V2.0 prediction for SKP1-like protein 1A (Q39255) · a predicted model of the same protein · chain A against A, TM-score 0.91
Q38825 · AlphaFold monomer V2.0 prediction for auxin-responsive protein IAA7 (Q38825) · a predicted model of the same protein · chain C against A, TM-score 0.27

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 Q39255
Every structure of UniProt Q570C0
Every structure of UniProt Q38825
Elsewhere: RCSB PDB 2P1O · PDBe 2P1O · UniProt Q39255 · UniProt Q570C0 · UniProt Q38825

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