MolNFT v1 · #71163 · protein
Crystal structure of dihydrodipicolinate synthase from campylobacter jejuni
3M5V: “Crystal structure of dihydrodipicolinate synthase from campylobacter jejuni”. X-ray diffraction, 2 ligands (CL, SO4), 8 pockets (best druggability 0.77). MolNFT v1 #71163 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3M5V
- Type
- protein
- Length
- 1,192 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
- CL, SO4
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 298 | 48% helix, 14% strand | Q9PPB4 |
| B | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 300 | 48% helix, 14% strand | Q9PPB4 |
| C | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 296 | 49% helix, 14% strand | Q9PPB4 |
Ligands and binding sites
- CL · Chloride ion · ion · 10 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 9 copies · chains A, C, B, D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains B, D, A, C
- FMT · Formic acid · additive · chains B, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 716 | 0.77 | 0.82 | 83 | SO4, PEG |
| 2 | 696 | 0.77 | 0.82 | 82 | SO4, PEG |
| 3 | 228 | 0.55 | 0.78 | 29 | SO4 |
| 4 | 196 | 0.54 | 0.78 | 30 | SO4 |
| 5 | 68 | 0.32 | 0.75 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1514 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1503 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1012 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 978 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 modified (engineered).
Compared structures
- 3M5V · Crystal Structure of Dihydrodipicolinate Synthase from Campylobacter 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 C 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 3M5V · PDBe 3M5V · UniProt Q9PPB4
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