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Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal

Analyse Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1TAE
Type: protein
Length: 1,284 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA ligase, NAD-dependent
EC: 6.5.1.2
UniProt: Q837V6
Ligands: NAD, NA, SO4
Pockets: 12 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	DNA ligase, NAD-dependent (EC 6.5.1.2)	protein	321	41% helix, 21% strand	Q837V6

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
NA · Sodium ion · metal · 2 copies · chains B, D
SO4 · Sulfate ion · ion · 24 copies · chains A, B, C, D

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

Pockets

12 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	1054	0.85	0.86	124	SO4, NAD
2	828	0.85	0.87	91	SO4, NAD
3	1093	0.82	0.83	103	SO4, NA, NAD
4	1165	0.82	0.83	112	SO4, NA, NAD
5	384	0.63	0.78	43	empty

Interfaces

4 interfaces between chains.

A–D · 913 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 666 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 641 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 88 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1TAE · Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal · the same entry in another collection · chain A against A, TM-score 1.00
Q837V6 · AlphaFold monomer V2.0 prediction for DNA ligase (Q837V6) · a predicted model of the same protein · chain A against A, TM-score 0.76

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 Q837V6
Elsewhere: RCSB PDB 1TAE · PDBe 1TAE · UniProt Q837V6

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