MolNFT v1 · #80293 · protein
Crystal structure of short chain dehydrogenase MAP_2410 from mycobacterium paratuberculosis bound to NAD
3TSC · Putative oxidoreductase: “Crystal structure of short chain dehydrogenase MAP_2410 from mycobacterium paratuberculosis bound to NAD”. X-ray diffraction, 1 ligand (NAD), 13 pockets (best druggability 0.88). MolNFT v1 #80293 on…
- PDB
- 3TSC
- Type
- protein
- Length
- 1,084 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative oxidoreductase
- UniProt
- Q73X99
- Ligands
- NAD
- Pockets
- 13 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Putative oxidoreductase | protein | 271 | 50% helix, 15% strand | Q73X99 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 603 | 0.88 | 0.93 | 50 | empty |
| 2 | 495 | 0.81 | 0.88 | 58 | NAD |
| 3 | 503 | 0.81 | 0.87 | 60 | NAD |
| 4 | 518 | 0.81 | 0.87 | 60 | NAD, MPD |
| 5 | 494 | 0.80 | 0.87 | 62 | NAD |
Interfaces
6 interfaces between chains.
- B–D · 1711 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1699 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1450 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1433 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 639 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3TSC · Crystal structure of short chain dehydrogenase MAP_2410 from Mycobacterium… · 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 Q73X99
- Elsewhere: RCSB PDB 3TSC · PDBe 3TSC · UniProt Q73X99
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