MolNFT v1 · #51672 · protein
Dihydropteroate synthase from streptococcus pneumoniae: complex with 6-hydroxymethyl-7,8-dihydropterin monophosphate
2VEG: “Dihydropteroate synthase from streptococcus pneumoniae: complex with 6-hydroxymethyl-7,8-dihydropterin…”. X-ray diffraction, 2 ligands (PMM, PO4), 3 pockets (best druggability 0.54). MolNFT v1 #51672 on GenesisL1: 3D structure…
- PDB
- 2VEG
- Type
- protein
- Length
- 554 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydropteroate synthase
- EC
- 2.5.1.15
- UniProt
- P59655
- Ligands
- PMM, PO4
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydropteroate synthase (EC 2.5.1.15) | protein | 279 | 50% helix, 14% strand | P59655 |
| B | Dihydropteroate synthase (EC 2.5.1.15) | protein | 275 | 49% helix, 14% strand | P59655 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.54 | 0.77 | 33 | empty |
| 2 | 227 | 0.53 | 0.77 | 31 | PMM |
| 3 | 195 | 0.52 | 0.78 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1590 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2VEG · Dihydropteroate synthase from Streptococcus pneumoniae: complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P59655 · AlphaFold monomer V2.0 prediction for dihydropteroate synthase (P59655) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P59655
- Elsewhere: RCSB PDB 2VEG · PDBe 2VEG · UniProt P59655
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