MolNFT v1 · #111632 · protein
Crystal structure of 4-hydroxy-tetrahydrodipicolinate reductase (htpa reductase) from pseudomonas aeruginosa
4YWJ: “Crystal structure of 4-hydroxy-tetrahydrodipicolinate reductase (htpa reductase) from pseudomonas aeruginosa”. X-ray diffraction, 2 ligands (NAD, CL), 6 pockets (best druggability 0.52). MolNFT v1 #111632 on GenesisL1: 3D structure…
- PDB
- 4YWJ
- Type
- protein
- Length
- 536 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxy-tetrahydrodipicolinate reductase
- EC
- 1.17.1.8
- UniProt
- P38103
- Ligands
- NAD, CL
- Pockets
- 6 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) | protein | 268 | 36% helix, 25% strand | P38103 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
- BU1 · 1,4-butanediol · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.52 | 0.83 | 24 | empty |
| 2 | 217 | 0.50 | 0.76 | 28 | NAD, PGE |
| 3 | 193 | 0.49 | 0.76 | 27 | NAD, PGE |
| 4 | 96 | 0.47 | 0.80 | 24 | empty |
| 5 | 93 | 0.36 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1440 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 4YWJ · Crystal structure of 4-hydroxy-tetrahydrodipicolinate reductase (HTPA reductase) from… · the same entry in another collection · chain A against A, TM-score 1.00
- P38103 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate reductase (P38103) · 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 P38103
- Elsewhere: RCSB PDB 4YWJ · PDBe 4YWJ · UniProt P38103
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