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mycobacterial DNA ligase D complexed with ATP and MES

Analyse mycobacterial DNA ligase D complexed with ATP and MES in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NHX
Type: protein
Length: 301 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.4
Source: Mycobacterium tuberculosis
Molecule: ATP-dependent DNA ligase
EC: 6.5.1.1
UniProt: A0A0T9BTX3
Ligands: ATP
Pockets: 2 · best druggability 0.70

Structure

x-ray diffraction · resolution 1.4 · 1 distinct chain · 21% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP-dependent DNA ligase (EC 6.5.1.1)	protein	301	21% helix, 38% strand	A0A0T9BTX3

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · chains A
MES · 2-(N-morpholino)-ethanesulfonic acid · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	456	0.70	0.81	43	ATP, MES
2	107	0.37	0.74	24	empty

Compared structures

6NHX · Mycobacterial DNA ligase D complexed with ATP and mes · 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 A0A0T9BTX3
Elsewhere: RCSB PDB 6NHX · PDBe 6NHX · UniProt A0A0T9BTX3

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