MolNFT v1 · #78740 · protein
Crystal structure of dihydrodipicolinate synthase from bartonella henselae
3SI9: “Crystal structure of dihydrodipicolinate synthase from bartonella henselae”. X-ray diffraction, 10 pockets (best druggability 0.77). MolNFT v1 #78740 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3SI9
- Type
- protein
- Length
- 1,174 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate synthase
- EC
- 4.2.1.52
- UniProt
- Q6G468
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 294 | 49% helix, 13% strand | Q6G468 |
| B, C | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 293 | 49% helix, 13% strand | Q6G468 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, C, B, 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 | 376 | 0.77 | 0.87 | 51 | EDO |
| 2 | 350 | 0.76 | 0.86 | 51 | empty |
| 3 | 253 | 0.57 | 0.78 | 31 | empty |
| 4 | 283 | 0.56 | 0.77 | 34 | empty |
| 5 | 266 | 0.56 | 0.77 | 35 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1438 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1429 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1011 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1011 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3SI9 · Crystal structure of Dihydrodipicolinate Synthase from Bartonella Henselae · the same entry in another collection · chain D against D, TM-score 1.00
- Q6G468 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate synthase (Q6G468) · a predicted model of the same protein · chain B 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 Q6G468
- Elsewhere: RCSB PDB 3SI9 · PDBe 3SI9 · UniProt Q6G468
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