MolNFT v1 · #17966 · protein
Structure of M. tuberculosis dihydrodipicolinate reductase in complex with NADH and 2,6 pdc
1P9L: “Structure of M. tuberculosis dihydrodipicolinate reductase in complex with NADH and 2,6 pdc”. X-ray diffraction, 2 ligands (NAI, PDC), 5 pockets (best druggability 0.75). MolNFT v1 #17966 on GenesisL1: 3D structure, binding sites…
- PDB
- 1P9L
- 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
- NAI, PDC
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydrodipicolinate reductase (EC 1.3.1.26) | protein | 245 | 36% helix, 26% strand | P72024 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 325 | 0.75 | 0.87 | 38 | NAI, PDC |
| 2 | 324 | 0.71 | 0.84 | 39 | NAI, PDC |
| 3 | 78 | 0.42 | 0.79 | 19 | empty |
| 4 | 62 | 0.38 | 0.79 | 16 | empty |
| 5 | 52 | 0.27 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1165 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 1P9L · Structure of M. tuberculosis dihydrodipicolinate reductase in complex with NADH and 2,6… · 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 1P9L · PDBe 1P9L · UniProt P72024
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