Research workbench
Legionella pneumophila dihydrodipicolinate synthase with first substrate pyruvate bound in the active site
Analyse Legionella pneumophila dihydrodipicolinate synthase with first substrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NQ1
- Type
- protein
- Length
- 580 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxy-tetrahydrodipicolinate synthase
- EC
- 4.2.1.52
- UniProt
- D5T7I7
- Ligands
- MG, CL
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.2.1.52) | protein | 290 | 50% helix, 14% strand | D5T7I7 |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains A, B
- CL · Chloride ion · ion · 6 copies · chains A, B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 522 | 0.79 | 0.86 | 54 | empty |
| 2 | 148 | 0.49 | 0.78 | 24 | CL |
| 3 | 129 | 0.46 | 0.78 | 21 | CL |
Interfaces
1 interface between chains.
- A–B · 1480 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 4NQ1 · Legionella pneumophila dihydrodipicolinate synthase with first substrate pyruvate bound… · 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 D5T7I7
- Elsewhere: RCSB PDB 4NQ1 · PDBe 4NQ1 · UniProt D5T7I7
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