MolNFT v1 · #170712 · protein

Tgt wt labelled mit 5F-TRP crystallised at pH 5.5

6YGP · Queuine tRNA-ribosyltransferase: “Tgt wt labelled mit 5F-TRP crystallised at pH 5.5”. X-ray diffraction, 2 ligands (ZN, CL), 3 pockets (best druggability 0.62). MolNFT v1 #170712 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6YGP
Type: protein
Length: 366 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Queuine tRNA-ribosyltransferase
EC: 2.4.2.29
UniProt: P28720
Ligands: ZN, CL
Pockets: 3 · best druggability 0.62

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Queuine tRNA-ribosyltransferase (EC 2.4.2.29)	protein	366	46% helix, 18% strand	P28720

Ligands and binding sites

ZN · Zinc ion · metal · chains A
CL · Chloride ion · ion · chains A
GOL · Glycerol · additive · 3 copies · chains A

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

Pockets

3 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	228	0.62	0.82	33	empty
2	74	0.33	0.75	19	empty
3	52	0.28	0.75	16	empty

Modifications

Observed in the structure: 4 modified (nonstandard).

Compared structures

6YGP · TGT WT labelled mit 5F-Trp crystallised at pH 5.5 · the same entry in another collection · chain A against A, 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 P28720
Elsewhere: RCSB PDB 6YGP · PDBe 6YGP · UniProt P28720

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