MolNFT v1 · #123905 · protein

Crystal structure of the covalent thioimide intermediate of the archaeosine synthase quef-like

5JYX · Archeaosine synthase quef-like: “Crystal structure of the covalent thioimide intermediate of the archaeosine synthase quef-like”. X-ray diffraction, 2 ligands (GD1, NA), 16 pockets (best druggability 0.74). MolNFT v1 #123905 on…

PDB: 5JYX
Type: protein
Length: 1,574 residues
Chains: 15
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Archeaosine synthase quef-like
UniProt: A3MSP1
Ligands: GD1, NA
Pockets: 16 · best druggability 0.74

Structure

x-ray diffraction · 8 distinct chains · 24% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, L	Archeaosine synthase quef-like	protein	105	24% helix, 45% strand	A3MSP1
B	Archeaosine synthase quef-like	protein	109	23% helix, 42% strand	A3MSP1
C, E, J, N	Archeaosine synthase quef-like	protein	104	24% helix, 43% strand	A3MSP1
F, H	Archeaosine synthase quef-like	protein	104	24% helix, 43% strand	A3MSP1
G, I	Archeaosine synthase quef-like	protein	107	23% helix, 43% strand	A3MSP1
K	Archeaosine synthase quef-like	protein	106	24% helix, 43% strand	A3MSP1
M	Archeaosine synthase quef-like	protein	103	24% helix, 43% strand	A3MSP1
O	Archeaosine synthase quef-like	protein	103	24% helix, 45% strand	A3MSP1

Ligands and binding sites

GD1 · 2-amino-5-[(Z)-iminomethyl]-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one · ligand · 15 copies · chains A, B, E, C, J, D, H, F, O, G, L, I, K, M, N
NA · Sodium ion · metal · 3 copies · chains C, E, L

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

Pockets

16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	388	0.74	0.85	64	empty
2	108	0.72	0.94	23	empty
3	161	0.69	0.89	34	empty
4	391	0.67	0.80	60	empty
5	54	0.67	0.96	19	empty

Interfaces

29 interfaces between chains.

E–F · 860 Å² buried · 12 hydrogen bonds · protein-protein
D–G · 851 Å² buried · 14 hydrogen bonds · protein-protein
C–J · 847 Å² buried · 12 hydrogen bonds · protein-protein
H–L · 840 Å² buried · 11 hydrogen bonds · protein-protein
I–O · 835 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 27 modified, 15 covalent (engineered, covalent ligand).

Compared structures

5JYX · Crystal structure of the covalent thioimide intermediate of the archaeosine synthase… · the same entry in another collection · chain O against O, 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 A3MSP1
Elsewhere: RCSB PDB 5JYX · PDBe 5JYX · UniProt A3MSP1

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