MolNFT v1 · #146214 · protein
Xanthomonas albilineans dihydropteroate synthase with 4-aminobenzoic acid at 1.65 a
6DAY: “Xanthomonas albilineans dihydropteroate synthase with 4-aminobenzoic acid at 1.65 a”. X-ray diffraction, 2 ligands (PAB, SO4), 8 pockets (best druggability 0.78). MolNFT v1 #146214 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6DAY
- Type
- protein
- Length
- 1,065 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydropteroate synthase
- EC
- 2.5.1.15
- UniProt
- D2UDM3
- Ligands
- PAB, SO4
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydropteroate synthase (EC 2.5.1.15) | protein | 259 | 48% helix, 17% strand | D2UDM3 |
| B | Dihydropteroate synthase (EC 2.5.1.15) | protein | 269 | 47% helix, 16% strand | D2UDM3 |
| C | Dihydropteroate synthase (EC 2.5.1.15) | protein | 264 | 47% helix, 16% strand | D2UDM3 |
| D | Dihydropteroate synthase (EC 2.5.1.15) | protein | 273 | 47% helix, 16% strand | D2UDM3 |
Ligands and binding sites
- PAB · 4-aminobenzoic acid · ligand · 8 copies · chains A, B, D, C
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.78 | 0.80 | 110 | PAB, SO4 |
| 2 | 1066 | 0.78 | 0.80 | 94 | PAB |
| 3 | 221 | 0.62 | 0.82 | 34 | PAB, SO4 |
| 4 | 251 | 0.61 | 0.80 | 34 | GOL |
| 5 | 260 | 0.58 | 0.79 | 37 | SO4 |
Interfaces
5 interfaces between chains.
- C–D · 1212 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1211 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 577 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 557 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 342 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6DAY · Xanthomonas albilineans Dihydropteroate synthase with 4-aminobenzoic acid at 1.65 A · 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 D2UDM3
- Elsewhere: RCSB PDB 6DAY · PDBe 6DAY · UniProt D2UDM3
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