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PB1 Domain of AtARF7 - SeMet Derivative

Analyse PB1 Domain of AtARF7 - SeMet Derivative in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4NJ7
Type: protein
Length: 1,216 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3
Source: Arabidopsis thaliana
Molecule: Auxin response factor 7
UniProt: P93022
Pockets: 16 · best druggability 0.72

Structure

x-ray diffraction · resolution 3 · 15 distinct chains · 29% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Auxin response factor 7	protein	77	27% helix, 27% strand	P93022
B	Auxin response factor 7	protein	78	27% helix, 31% strand	P93022
C, O	Auxin response factor 7	protein	80	33% helix, 25% strand	P93022
D	Auxin response factor 7	protein	70	30% helix, 27% strand	P93022
E	Auxin response factor 7	protein	79	24% helix, 28% strand	P93022
F	Auxin response factor 7	protein	81	28% helix, 30% strand	P93022
G	Auxin response factor 7	protein	78	27% helix, 27% strand	P93022
H	Auxin response factor 7	protein	76	30% helix, 26% strand	P93022
I	Auxin response factor 7	protein	79	29% helix, 27% strand	P93022
J	Auxin response factor 7	protein	74	32% helix, 27% strand	P93022
K	Auxin response factor 7	protein	75	25% helix, 32% strand	P93022
L	Auxin response factor 7	protein	71	27% helix, 27% strand	P93022
M	Auxin response factor 7	protein	72	29% helix, 28% strand	P93022
N	Auxin response factor 7	protein	69	35% helix, 25% strand	P93022
P	Auxin response factor 7	protein	77	27% helix, 29% strand	P93022

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	652	0.72	0.79	59	empty
2	699	0.70	0.77	69	empty
3	637	0.62	0.74	65	empty
4	459	0.59	0.75	40	empty
5	310	0.52	0.74	40	empty

Interfaces

29 interfaces between chains.

C–P · 477 Å² buried · 8 hydrogen bonds · protein-protein
J–O · 453 Å² buried · 6 hydrogen bonds · protein-protein
B–N · 451 Å² buried · 7 hydrogen bonds · protein-protein
B–K · 445 Å² buried · 8 hydrogen bonds · protein-protein
H–L · 443 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 23 modified (engineered).

Compared structures

4NJ7 · PB1 domain of ATARF7 - semet derivative · the same entry in another collection · chain K against K, TM-score 1.00

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 P93022
Elsewhere: RCSB PDB 4NJ7 · PDBe 4NJ7 · UniProt P93022

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