Research workbench

QRI7 and AMP complex

Analyse QRI7 and AMP complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3WUH
Type: protein
Length: 694 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRNA N6-adenosine threonylcarbamoyltransferase, mitochondrial
EC: 2.3.1.-
UniProt: P43122
Ligands: AMP, ZN
Pockets: 4 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	TRNA N6-adenosine threonylcarbamoyltransferase, mitochondrial (EC 2.3.1.-)	protein	344	42% helix, 21% strand	P43122
B	TRNA N6-adenosine threonylcarbamoyltransferase, mitochondrial (EC 2.3.1.-)	protein	350	41% helix, 21% strand	P43122

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	768	0.78	0.82	103	AMP
2	398	0.66	0.80	48	AMP
3	86	0.56	0.86	15	empty
4	60	0.29	0.74	18	empty

Interfaces

1 interface between chains.

A–B · 1170 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

3WUH · Qri7 and AMP complex · the same entry in another collection · chain A against A, TM-score 1.00
P43122 · AlphaFold monomer V2.0 prediction for tRNA N6-adenosine threonylcarbamoyltransferase… · a predicted model of the same protein · chain B 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 P43122
Elsewhere: RCSB PDB 3WUH · PDBe 3WUH · UniProt P43122

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