MolNFT v1 · #168594 · protein

Crystal structure of the zeitlupe light-state mimic G46A

6WLE · Adagio protein 1: “Crystal structure of the zeitlupe light-state mimic G46A”. X-ray diffraction, 1 ligand (FMN), 14 pockets (best druggability 0.73). MolNFT v1 #168594 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6WLE
Type: protein
Length: 912 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adagio protein 1
UniProt: Q94BT6
Ligands: FMN
Pockets: 14 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 21% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A, D, E, G	Adagio protein 1	protein	130	22% helix, 32% strand	Q94BT6
C	Adagio protein 1	protein	131	18% helix, 32% strand	Q94BT6
F	Adagio protein 1	protein	131	22% helix, 31% strand	Q94BT6

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · 7 copies · chains B, A, C, D, E, F, G
EDO · 1,2-ethanediol · additive · 3 copies · chains C, D, E

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

Pockets

14 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	187	0.73	0.90	23	FMN
2	188	0.72	0.89	26	FMN
3	176	0.71	0.89	23	FMN
4	180	0.71	0.88	24	FMN
5	174	0.70	0.88	23	FMN

Interfaces

5 interfaces between chains.

C–G · 1092 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 1054 Å² buried · 8 hydrogen bonds · protein-protein
A–E · 1018 Å² buried · 6 hydrogen bonds · protein-protein
B–F · 380 Å² buried · 2 hydrogen bonds · protein-protein
F–G · 39 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

6WLE · Crystal structure of the Zeitlupe light-state mimic G46A · the same entry in another collection · chain G against G, TM-score 1.00
Q94BT6 · AlphaFold monomer V2.0 prediction for adagio protein 1 (Q94BT6) · a predicted model of the same protein · chain G against A, TM-score 0.91

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 6WLE · PDBe 6WLE · UniProt Q94BT6

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