Research workbench
Structure of M. tuberculosis dihydrodipicolinate reductase in complex with NADH and 2,6 pdc
Analyse Structure of M. tuberculosis dihydrodipicolinate reductase in complex with NADH… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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