MolNFT v1 · #136431 · protein
The crystal structure of 7,8-dihydropteroate synthase from vibrio fischeri ES114
5USW: “The crystal structure of 7,8-dihydropteroate synthase from vibrio fischeri ES114”. X-ray diffraction, 9 pockets (best druggability 0.60). MolNFT v1 #136431 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5USW
- Type
- protein
- Length
- 1,091 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydropteroate synthase
- EC
- 2.5.1.15
- UniProt
- Q5E7M1
- Pockets
- 9 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydropteroate synthase (EC 2.5.1.15) | protein | 279 | 45% helix, 16% strand | Q5E7M1 |
| B | Dihydropteroate synthase (EC 2.5.1.15) | protein | 270 | 46% helix, 19% strand | Q5E7M1 |
| C | Dihydropteroate synthase (EC 2.5.1.15) | protein | 272 | 46% helix, 17% strand | Q5E7M1 |
| D | Dihydropteroate synthase (EC 2.5.1.15) | protein | 270 | 46% helix, 20% strand | Q5E7M1 |
Ligands and binding sites
- GOL · Glycerol · additive · 9 copies · chains A, B, C, D
- FMT · Formic acid · additive · 4 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 455 | 0.60 | 0.75 | 64 | GOL |
| 2 | 284 | 0.60 | 0.79 | 43 | FMT |
| 3 | 189 | 0.55 | 0.79 | 34 | GOL |
| 4 | 180 | 0.45 | 0.75 | 33 | GOL |
| 5 | 106 | 0.40 | 0.77 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1312 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 1301 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 285 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 189 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified (engineered).
Compared structures
- 5USW · The crystal structure of 7,8-dihydropteroate synthase from Vibrio fischeri ES114 · 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 Q5E7M1
- Elsewhere: RCSB PDB 5USW · PDBe 5USW · UniProt Q5E7M1
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