MolNFT v1 · #91124 · protein
X-ray crystal structure of dihydrodipicolinate reductase from burkholderia thailandensis
4F3Y: “X-ray crystal structure of dihydrodipicolinate reductase from burkholderia thailandensis”. X-ray diffraction, 3 ligands (NA, UNX, CL), 8 pockets (best druggability 0.42). MolNFT v1 #91124 on GenesisL1: 3D structure, binding sites…
- PDB
- 4F3Y
- Type
- protein
- Length
- 532 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate reductase
- EC
- 1.3.1.26
- UniProt
- Q2SZ94
- Ligands
- NA, UNX, CL
- Pockets
- 8 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrodipicolinate reductase (EC 1.3.1.26) | protein | 267 | 35% helix, 24% strand | Q2SZ94 |
| B | Dihydrodipicolinate reductase (EC 1.3.1.26) | protein | 265 | 37% helix, 25% strand | Q2SZ94 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B
- UNX · Unknown atom or ion · ion · 10 copies · chains A, B
- 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
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.42 | 0.75 | 22 | empty |
| 2 | 67 | 0.39 | 0.79 | 17 | empty |
| 3 | 57 | 0.38 | 0.80 | 18 | empty |
| 4 | 79 | 0.37 | 0.77 | 19 | empty |
| 5 | 95 | 0.32 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1359 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4F3Y · X-Ray Crystal Structure of Dihydrodipicolinate reductase from Burkholderia thailandensis · the same entry in another collection · chain A against A, TM-score 1.00
- Q2SZ94 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate reductase (Q2SZ94) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q2SZ94
- Elsewhere: RCSB PDB 4F3Y · PDBe 4F3Y · UniProt Q2SZ94
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