MolNFT v1 · #152700 · protein

Crystal structure of arabidopsis thaliana profilin 3

6IQK · Profilin-5: “Crystal structure of arabidopsis thaliana profilin 3”. X-ray diffraction, 20 pockets (best druggability 0.75). MolNFT v1 #152700 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6IQK
Type: protein
Length: 1,641 residues
Chains: 11
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Profilin-5; ATPRF3
UniProt: Q9FE63
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 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	898	0.75	0.78	93	empty
2	411	0.64	0.78	42	empty
3	66	0.60	0.90	20	empty
4	368	0.60	0.76	41	empty
5	71	0.59	0.90	19	empty

Interfaces

16 interfaces between chains.

E–I · 616 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 · 553 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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