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crystal structure of Arabidopsis thaliana Profilin 3

Analyse crystal structure of Arabidopsis thaliana Profilin 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6IQK
Type: protein
Length: 1,641 residues
Chains: 11
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.6
Source: Arabidopsis thaliana
Molecule: Profilin-5; AtPRF3
UniProt: Q9FE63
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · resolution 3.6 · 5 distinct chains · 23% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Profilin-5	protein	137	31% helix, 32% strand	Q9FE63
B, D	Profilin-5	protein	138	30% helix, 32% strand	Q9FE63
F, J, H	Profilin-5	protein	139	28% helix, 32% strand	Q9FE63
I	Profilin-5	protein	136	28% helix, 30% strand	Q9FE63
K	AtPRF3	protein	264	9% helix, 2% strand	—

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	897	0.75	0.78	92	empty
2	412	0.64	0.78	42	empty
3	66	0.60	0.90	20	empty
4	367	0.60	0.76	41	empty
5	71	0.59	0.90	19	empty

Interfaces

16 interfaces between chains.

E–I · 617 Å² buried · 10 hydrogen bonds · protein-protein
A–G · 606 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 574 Å² buried · 2 hydrogen bonds · protein-protein
F–H · 560 Å² buried · 7 hydrogen bonds · protein-protein
D–H · 554 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

6IQK · Crystal structure of arabidopsis thaliana profilin 3 · the same entry in another collection · chain K against K, TM-score 1.00
Q9FE63 · AlphaFold monomer V2.0 prediction for profilin-3 (Q9FE63) · a predicted model of the same protein · chain I against A, TM-score 0.94

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 Q9FE63
Elsewhere: RCSB PDB 6IQK · PDBe 6IQK · UniProt Q9FE63

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