MolNFT v1 · #28011 · protein

X-ray structure of gene product from arabidopsis thaliana AT3G21360

1Y0Z · Protein product of AT3G21360: “X-ray structure of gene product from arabidopsis thaliana AT3G21360”. X-ray diffraction, 2 ligands (FE2, SO4), 7 pockets (best druggability 0.85). MolNFT v1 #28011 on GenesisL1: 3D structure, binding…

PDB: 1Y0Z
Type: protein
Length: 643 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein product of AT3G21360
UniProt: Q9LIG0
Ligands: FE2, SO4
Pockets: 7 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein product of AT3G21360	protein	321	28% helix, 29% strand	Q9LIG0
B	Protein product of AT3G21360	protein	322	28% helix, 27% strand	Q9LIG0

Ligands and binding sites

FE2 · Fe (II) ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 4 copies · chains A, B

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

Pockets

7 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	1195	0.85	0.86	117	SO4, FE2
2	65	0.44	0.82	14	empty
3	64	0.40	0.80	13	empty
4	120	0.40	0.75	20	empty
5	80	0.38	0.77	16	empty

Interfaces

1 interface between chains.

A–B · 722 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

1Y0Z · X-ray structure of gene product from Arabidopsis thaliana At3g21360 · the same entry in another collection · chain A against A, TM-score 1.00
Q9LIG0 · AlphaFold monomer V2.0 prediction for clavaminate synthase-like protein AT3G21360 (Q9LIG0) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q9LIG0
Elsewhere: RCSB PDB 1Y0Z · PDBe 1Y0Z · UniProt Q9LIG0

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