Research workbench

Structure of DNA ligase a from mycobacterium tuberculosis bound to NAD

Analyse Structure of DNA ligase a from mycobacterium tuberculosis bound to NAD in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7K72
Type: protein
Length: 1,271 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA ligase a
EC: 6.5.1.2
UniProt: P9WNV1
Ligands: NAD, MG, CA
Pockets: 8 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	DNA ligase a (EC 6.5.1.2)	protein	318	41% helix, 23% strand	P9WNV1
B	DNA ligase a (EC 6.5.1.2)	protein	317	39% helix, 23% strand	P9WNV1

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 9 copies · chains A, B, C, D
CA · Calcium ion · metal · 2 copies · chains A, B
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains A, B, C, D

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

Pockets

8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1006	0.84	0.85	115	NAD, MG, MPD
2	1098	0.84	0.85	127	NAD, MG, CA, MPD
3	1004	0.83	0.84	96	NAD, MG, CA, MPD
4	1128	0.82	0.83	107	NAD, MG, MPD
5	558	0.75	0.83	52	empty

Interfaces

3 interfaces between chains.

A–B · 862 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 411 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 122 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7K72 · Structure of DNA ligase A from Mycobacterium tuberculosis bound to NAD · the same entry in another collection · chain D against D, TM-score 1.00
P9WNV1 · AlphaFold monomer V2.0 prediction for DNA ligase a (P9WNV1) · a predicted model of the same protein · chain B against A, TM-score 0.77

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 P9WNV1
Elsewhere: RCSB PDB 7K72 · PDBe 7K72 · UniProt P9WNV1

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.