MolNFT v1 · #70037 · protein
Crystal structure of D,D-heptose 1.7-bisphosphate phosphatase from B. bronchiseptica complexed with magnesium and phosphate
3L8H · Putative haloacid dehalogenase-like hydrolase: “Crystal structure of D,D-heptose 1.7-bisphosphate phosphatase from B. bronchiseptica complexed with magnesium…”. X-ray diffraction, 5 ligands (FX1, SAR, MG), 7 pockets (best…
- PDB
- 3L8H
- Type
- protein
- Length
- 716 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative haloacid dehalogenase-like hydrolase
- UniProt
- Q7WG29
- Ligands
- FX1, SAR, MG, ZN, PO4
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Putative haloacid dehalogenase-like hydrolase | protein | 179 | 37% helix, 18% strand | Q7WG29 |
Ligands and binding sites
- FX1 · beta-D-threo-hexo-2,4-diulo-2,5-furanose · ligand · chains C
- SAR · Sarcosine · ligand · chains D
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 5 copies · chains A, B, C, D
- FMT · Formic acid · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 447 | 0.64 | 0.77 | 35 | empty |
| 2 | 197 | 0.58 | 0.81 | 25 | MG, PO4, FMT |
| 3 | 146 | 0.58 | 0.84 | 22 | MG, PO4, FX1 |
| 4 | 130 | 0.56 | 0.83 | 21 | MG, PO4, SAR |
| 5 | 137 | 0.52 | 0.81 | 21 | PO4 |
Interfaces
3 interfaces between chains.
- A–C · 685 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 684 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 488 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3L8H · Crystal Structure of D,D-heptose 1.7-bisphosphate phosphatase from B. bronchiseptica… · the same entry in another collection · chain D against D, TM-score 1.00
- Q7WG29 · AlphaFold monomer V2.0 prediction for D-glycero-beta-D-manno- heptose-1,7-bisphosphate… · 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 Q7WG29
- Elsewhere: RCSB PDB 3L8H · PDBe 3L8H · UniProt Q7WG29
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.