Research workbench
Dihydrodipicolinate reductase from mycobacterium tuberculosis complexed with NADPH and pdc
Analyse Dihydrodipicolinate reductase from mycobacterium tuberculosis complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1C3V
- Type
- protein
- Length
- 490 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate reductase
- EC
- 1.3.1.26
- UniProt
- P72024
- Ligands
- NDP, PDC
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydrodipicolinate reductase (EC 1.3.1.26) | protein | 245 | 34% helix, 25% strand | P72024 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- PDC · Pyridine-2,6-dicarboxylic acid · ligand · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.74 | 0.85 | 44 | NDP, PDC |
| 2 | 297 | 0.73 | 0.86 | 35 | NDP, PDC |
| 3 | 91 | 0.41 | 0.78 | 21 | empty |
| 4 | 66 | 0.40 | 0.80 | 16 | empty |
| 5 | 78 | 0.39 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1187 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 1C3V · Dihydrodipicolinate reductase from mycobacterium tuberculosis complexed with NADPH and pdc · 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 P72024
- Elsewhere: RCSB PDB 1C3V · PDBe 1C3V · UniProt P72024
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