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Structure of the GAR1 domain of NAF1

Analyse Structure of the GAR1 domain of NAF1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2V3M
Type: protein
Length: 567 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NAF1
UniProt: P53919
Ligands: SO4
Pockets: 6 · best druggability 0.79

Structure

x-ray diffraction · 5 distinct chains · 12% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NAF1	protein	94	12% helix, 40% strand	P53919
B	NAF1	protein	86	13% helix, 38% strand	P53919
C, E	NAF1	protein	101	11% helix, 37% strand	P53919
D	NAF1	protein	94	12% helix, 39% strand	P53919
F	NAF1	protein	91	12% helix, 43% strand	P53919

Ligands and binding sites

SO4 · Sulfate ion · ion · 7 copies · chains A, F, B, E, C, D

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1001	0.79	0.80	98	empty
2	372	0.68	0.81	36	SO4
3	65	0.41	0.80	17	empty
4	55	0.38	0.80	13	empty
5	63	0.34	0.77	19	empty

Interfaces

7 interfaces between chains.

C–D · 617 Å² buried · 8 hydrogen bonds · protein-protein
B–E · 581 Å² buried · 7 hydrogen bonds · protein-protein
C–F · 562 Å² buried · 5 hydrogen bonds · protein-protein
A–F · 551 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 443 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 modified (engineered).

Compared structures

2V3M · Structure of the Gar1 domain of NAf1 · the same entry in another collection · chain F against F, TM-score 1.00
P53919 · AlphaFold monomer V2.0 prediction for H/ACA ribonucleoprotein complex non-core subunit… · a predicted model of the same protein · chain B against A, TM-score 0.97

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 P53919
Elsewhere: RCSB PDB 2V3M · PDBe 2V3M · UniProt P53919

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