MolNFT v1 · #22613 · protein
Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal
1TAE · DNA ligase, NAD-dependent: “Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal”. X-ray diffraction, 3 ligands (NAD, NA, SO4), 12 pockets (best druggability 0.85). MolNFT v1 #22613 on…
- 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.
| Volume (ų) | 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 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 666 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 641 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 88 Ų 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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