MolNFT v1 · #159982 · protein

Queuine lyase from clostridium spiroforme bound to SAM and queuine

6P78: “Queuine lyase from clostridium spiroforme bound to SAM and queuine”. X-ray diffraction, 3 ligands (SF4, QUG, SAM), 2 pockets (best druggability 0.84). MolNFT v1 #159982 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6P78
Type: protein
Length: 230 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Queuine lyase
UniProt: B1C2R2
Ligands: SF4, QUG, SAM
Pockets: 2 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Queuine lyase	protein	230	39% helix, 20% strand	B1C2R2

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · chains A
QUG · 2-amino-5-({[(1S,4S,5S)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-1,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one · ligand · chains A
SAM · S-adenosylmethionine · ligand · chains A

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

Pockets

2 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	440	0.84	0.92	49	SF4, QUG, SAM
2	58	0.35	0.78	11	empty

Modifications

Observed in the structure: 1 modified (methylation).

Compared structures

6P78 · queuine lyase from Clostridium spiroforme bound to SAM and queuine · 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 B1C2R2
Elsewhere: RCSB PDB 6P78 · PDBe 6P78 · UniProt B1C2R2

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