MolNFT v1 · #93900 · protein
Crystal structure of 2-keto-3-deoxyoctulosonate 8-phosphate phosphohydrolase from bacteroides thetaiotaomicron
4HGN · 2-keto-3-deoxy-D-manno-octulosonate 8-phosphate…: “Crystal structure of 2-keto-3-deoxyoctulosonate 8-phosphate phosphohydrolase from bacteroides thetaiotaomicron”. X-ray diffraction, 1 ligand (MG), 7 pockets (best druggability…
- PDB
- 4HGN
- Type
- protein
- Length
- 659 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-keto-3-deoxy-D-manno-octulosonate 8-phosphate phosphohydrolase
- EC
- 3.1.3.45
- UniProt
- Q8A748
- Ligands
- MG
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | 2-keto-3-deoxy-D-manno-octulosonate 8-phosphate phosphohydrolase (EC 3.1.3.45) | protein | 165 | 39% helix, 19% strand | Q8A748 |
| B | 2-keto-3-deoxy-D-manno-octulosonate 8-phosphate phosphohydrolase (EC 3.1.3.45) | protein | 164 | 38% helix, 21% strand | Q8A748 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- FMT · Formic acid · additive · 2 copies · chains B, D, C
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 | 967 | 0.75 | 0.78 | 96 | FMT |
| 2 | 285 | 0.61 | 0.79 | 25 | MG |
| 3 | 292 | 0.60 | 0.79 | 37 | MG |
| 4 | 289 | 0.59 | 0.78 | 30 | empty |
| 5 | 246 | 0.58 | 0.79 | 26 | empty |
Interfaces
4 interfaces between chains.
- A–C · 879 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 848 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 825 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 824 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4HGN · Crystal Structure of 2-keto-3-deoxyoctulosonate 8-phosphate PHOSPHOHYDROLASE from… · 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 Q8A748
- Elsewhere: RCSB PDB 4HGN · PDBe 4HGN · UniProt Q8A748
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