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Dihydrodipicolinate synthase from C. jejuni with vacant active site and vacant allosteric site
Analyse Dihydrodipicolinate synthase from C. jejuni with vacant active site and vacant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R53
- Type
- protein
- Length
- 1,183 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxy-tetrahydrodipicolinate synthase
- EC
- 4.3.3.7
- UniProt
- Q9PPB4
- Ligands
- CL
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 296 | 48% helix, 14% strand | Q9PPB4 |
| B, C | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 295 | 48% helix, 14% strand | Q9PPB4 |
| D | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 297 | 48% helix, 14% strand | Q9PPB4 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains B, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, D, C
- PGE · Triethylene glycol · additive · 3 copies · chains B, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, C
- PG4 · Tetraethylene glycol · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 456 | 0.76 | 0.85 | 50 | empty |
| 2 | 420 | 0.76 | 0.85 | 50 | empty |
| 3 | 181 | 0.54 | 0.79 | 32 | CL |
| 4 | 203 | 0.54 | 0.78 | 26 | empty |
| 5 | 183 | 0.54 | 0.79 | 28 | CL |
Interfaces
4 interfaces between chains.
- C–D · 1472 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1468 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1045 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1041 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4R53 · dihydrodipicolinate synthase from C. jejuni with vacant active site and vacant allosteric… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9PPB4 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate synthase (Q9PPB4) · a predicted model of the same protein · chain B 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 Q9PPB4
- Elsewhere: RCSB PDB 4R53 · PDBe 4R53 · UniProt Q9PPB4
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