MolNFT v1 · #136042 · protein
Dapb from mycobacterium tuberculosis
5UGV · 4-hydroxy-tetrahydrodipicolinate reductase: “Dapb from mycobacterium tuberculosis”. X-ray diffraction, 2 ligands (NAD, SO4), 6 pockets (best druggability 0.58). MolNFT v1 #136042 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5UGV
- Type
- protein
- Length
- 489 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxy-tetrahydrodipicolinate reductase
- EC
- 1.17.1.8
- UniProt
- A5U6C6
- Ligands
- NAD, SO4
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) | protein | 245 | 36% helix, 27% strand | A5U6C6 |
| B | 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) | protein | 244 | 35% helix, 27% strand | A5U6C6 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.58 | 0.78 | 29 | SO4 |
| 2 | 281 | 0.57 | 0.77 | 31 | empty |
| 3 | 128 | 0.48 | 0.78 | 22 | empty |
| 4 | 106 | 0.41 | 0.76 | 14 | empty |
| 5 | 70 | 0.30 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1242 Ų buried · 22 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 A5U6C6
- Elsewhere: RCSB PDB 5UGV · PDBe 5UGV · UniProt A5U6C6
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