MolNFT v1 · #179487 · protein
Structure of DNA ligase a from mycobacterium tuberculosis bound to NAD
7K72: “Structure of DNA ligase a from mycobacterium tuberculosis bound to NAD”. X-ray diffraction, 3 ligands (NAD, MG, CA), 8 pockets (best druggability 0.84). MolNFT v1 #179487 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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.
| Volume (ų) | 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 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 411 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 122 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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
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