MolNFT v1 · #66170 · protein
Crystal structure of dihydrodipicolinate synthase from bacillus anthracis in complex with its substrate, pyruvate
3HIJ: “Crystal structure of dihydrodipicolinate synthase from bacillus anthracis in complex with its substrate…”. X-ray diffraction, 1 ligand (NA), 11 pockets (best druggability 0.73). MolNFT v1 #66170 on GenesisL1: 3D structure, binding…
- PDB
- 3HIJ
- Type
- protein
- Length
- 1,168 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate synthase
- UniProt
- Q81WN7
- Ligands
- NA
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Dihydrodipicolinate synthase | protein | 292 | 50% helix, 13% strand | Q81WN7 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.73 | 0.82 | 52 | empty |
| 2 | 462 | 0.71 | 0.82 | 39 | empty |
| 3 | 227 | 0.54 | 0.77 | 35 | empty |
| 4 | 203 | 0.53 | 0.78 | 31 | empty |
| 5 | 215 | 0.52 | 0.77 | 37 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1436 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1416 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 967 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 963 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 3HIJ · Crystal structure of dihydrodipicolinate synthase from Bacillus anthracis in complex with… · the same entry in another collection · chain A 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 Q81WN7
- Elsewhere: RCSB PDB 3HIJ · PDBe 3HIJ · UniProt Q81WN7
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