Research workbench
Characterisation of the first monomeric dihydrodipicolinate synthase variant reveals evolutionary insights
Analyse Characterisation of the first monomeric dihydrodipicolinate synthase variant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PB2
- Type
- protein
- Length
- 1,784 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate synthase
- EC
- 4.2.1.52
- UniProt
- Q9X1K9
- Pockets
- 17 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 300 | 50% helix, 14% strand | Q9X1K9 |
| B, D | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 298 | 52% helix, 14% strand | Q9X1K9 |
| C | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 297 | 51% helix, 14% strand | Q9X1K9 |
| E | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 296 | 50% helix, 14% strand | Q9X1K9 |
| F | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 295 | 51% helix, 14% strand | Q9X1K9 |
Ligands and binding sites
- GOL · Glycerol · additive · 15 copies · chains A, B, E, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 630 | 0.74 | 0.81 | 62 | empty |
| 2 | 567 | 0.73 | 0.81 | 63 | GOL |
| 3 | 173 | 0.55 | 0.80 | 32 | empty |
| 4 | 183 | 0.53 | 0.78 | 29 | empty |
| 5 | 148 | 0.53 | 0.80 | 25 | GOL |
Interfaces
6 interfaces between chains.
- A–B · 1456 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 1445 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 780 Ų buried · 20 hydrogen bonds · protein-protein
- A–E · 769 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 766 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3PB2 · Characterisation of the first monomeric dihydrodipicolinate synthase variant reveals… · the same entry in another collection · chain F against F, TM-score 1.00
- Q9X1K9 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate synthase (Q9X1K9) · a predicted model of the same protein · chain F against A, TM-score 0.99
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 Q9X1K9
- Elsewhere: RCSB PDB 3PB2 · PDBe 3PB2 · UniProt Q9X1K9
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