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Complex of HI0065 with ADP and magnesium

Analyse Complex of HI0065 with ADP and magnesium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1HTW
Type: protein
Length: 474 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HI0065
UniProt: P44492
Ligands: ADP, MG, NA
Pockets: 2 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	HI0065	protein	158	32% helix, 29% strand	P44492

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
MG · Magnesium ion · metal · 4 copies · chains A, B, C
NA · Sodium ion · metal · 3 copies · chains A, B, C
ACT · Acetate ion · additive · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	98	0.48	0.81	29	empty
2	61	0.31	0.75	17	empty

Interfaces

3 interfaces between chains.

A–C · 806 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 792 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 30 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1HTW · Complex of HI0065 with ADP and magnesium · the same entry in another collection · chain A against A, TM-score 1.00
P44492 · AlphaFold monomer V2.0 prediction for tRNA threonylcarbamoyladenosine biosynthesis… · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P44492
Elsewhere: RCSB PDB 1HTW · PDBe 1HTW · UniProt P44492

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