Research workbench
Crystal structure of dihydrodipicolinate reductase from bartonella henselae at 2.0A resolution
Analyse Crystal structure of dihydrodipicolinate reductase from bartonella henselae at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IJP
- Type
- protein
- Length
- 533 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate reductase
- EC
- 1.3.1.26
- UniProt
- Q6G2G3
- Ligands
- NAP, NA, UNX, CL
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrodipicolinate reductase (EC 1.3.1.26) | protein | 266 | 37% helix, 25% strand | Q6G2G3 |
| B | Dihydrodipicolinate reductase (EC 1.3.1.26) | protein | 267 | 36% helix, 25% strand | Q6G2G3 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- NA · Sodium ion · metal · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 4 copies · chains A
- CL · Chloride ion · ion · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 374 | 0.73 | 0.84 | 46 | CL, NAP, UNX |
| 2 | 244 | 0.51 | 0.75 | 29 | empty |
| 3 | 155 | 0.50 | 0.78 | 27 | empty |
| 4 | 144 | 0.48 | 0.78 | 17 | empty |
| 5 | 91 | 0.35 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 206 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3IJP · Crystal structure of dihydrodipicolinate reductase from bartonella henselae at 2.0A… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6G2G3 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate reductase (Q6G2G3) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q6G2G3
- Elsewhere: RCSB PDB 3IJP · PDBe 3IJP · UniProt Q6G2G3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.