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Light-state structure of arabidopsis thaliana zeitlupe

Analyse Light-state structure of arabidopsis thaliana zeitlupe in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5SVW
Type: protein
Length: 490 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adagio protein 1
UniProt: Q94BT6
Ligands: FMN
Pockets: 7 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 24% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Adagio protein 1	protein	134	23% helix, 31% strand	Q94BT6
A	Adagio protein 1	protein	116	24% helix, 34% strand	Q94BT6
C	Adagio protein 1	protein	118	25% helix, 37% strand	Q94BT6
D	Adagio protein 1	protein	122	24% helix, 34% strand	Q94BT6

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · 4 copies · chains B, A, C, D

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

Pockets

7 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	511	0.79	0.86	63	FMN
2	561	0.73	0.81	40	empty
3	186	0.70	0.88	25	FMN
4	179	0.70	0.88	24	FMN
5	174	0.54	0.80	29	empty

Interfaces

5 interfaces between chains.

B–A · 1281 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 621 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 601 Å² buried · 1 hydrogen bond · protein-protein
A–C · 131 Å² buried · 1 hydrogen bond · protein-protein
B–D · 36 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 cofactor (flavinylation).

Compared structures

5SVW · Light-state Structure of Arabidopsis Thaliana Zeitlupe · the same entry in another collection · chain D against D, TM-score 1.00
Q94BT6 · AlphaFold monomer V2.0 prediction for adagio protein 1 (Q94BT6) · a predicted model of the same protein · chain C 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 Q94BT6
Elsewhere: RCSB PDB 5SVW · PDBe 5SVW · UniProt Q94BT6

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