MolNFT v1 · #74924 · protein
Characterisation of the first monomeric dihydrodipicolinate synthase variant reveals evolutionary insights
3PB0: “Characterisation of the first monomeric dihydrodipicolinate synthase variant reveals evolutionary insights”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.82). MolNFT v1 #74924 on GenesisL1: 3D structure, binding…
- PDB
- 3PB0
- Type
- protein
- Length
- 1,200 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate synthase
- EC
- 4.2.1.52
- UniProt
- Q9X1K9
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 300 | 52% helix, 14% strand | Q9X1K9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, C, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1018 | 0.82 | 0.83 | 110 | empty |
| 2 | 806 | 0.75 | 0.79 | 78 | empty |
| 3 | 432 | 0.64 | 0.77 | 61 | empty |
| 4 | 371 | 0.61 | 0.77 | 52 | empty |
| 5 | 217 | 0.58 | 0.80 | 42 | empty |
Interfaces
5 interfaces between chains.
- A–C · 678 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 340 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 237 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 138 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 128 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3PB0 · Characterisation of the first monomeric dihydrodipicolinate synthase variant reveals… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9X1K9 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate synthase (Q9X1K9) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 3PB0 · PDBe 3PB0 · UniProt Q9X1K9
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