Research workbench
Crystal structure of dihydrodipicolinate synthase from campylobacter jejuni subsp. jejuni nctc 11168
Analyse Crystal structure of dihydrodipicolinate synthase from campylobacter jejuni… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LER
- Type
- protein
- Length
- 1,190 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate synthase
- EC
- 4.2.1.52
- UniProt
- Q9PPB4
- Ligands
- MG
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 298 | 47% helix, 14% strand | Q9PPB4 |
| C | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 296 | 47% helix, 14% strand | Q9PPB4 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B, C
- FMT · Formic acid · additive · chains B, C
- PEG · Di(hydroxyethyl)ether · additive · chains B
- ACY · Acetic acid · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.75 | 0.86 | 51 | empty |
| 2 | 372 | 0.73 | 0.85 | 52 | empty |
| 3 | 154 | 0.52 | 0.79 | 28 | empty |
| 4 | 151 | 0.51 | 0.79 | 27 | empty |
| 5 | 155 | 0.51 | 0.79 | 23 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1514 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1511 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 998 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 975 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 31 modified (engineered, nonstandard).
Compared structures
- 3LER · Crystal Structure of Dihydrodipicolinate Synthase from Campylobacter jejuni subsp. jejuni… · 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 D 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 3LER · PDBe 3LER · UniProt Q9PPB4
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