Research workbench
Xanthomonas albilineans dihydropteroate synthase in complex with (indole-2-carboxylic acid) and (6-chloroguanine)
Analyse Xanthomonas albilineans dihydropteroate synthase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q62
- Type
- protein
- Length
- 1,064 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
- 6GU, ICB, SO4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydropteroate synthase (EC 2.5.1.15) | protein | 269 | 48% helix, 16% strand | D2UDM3 |
| C | Dihydropteroate synthase (EC 2.5.1.15) | protein | 268 | 48% helix, 16% strand | D2UDM3 |
| B | Dihydropteroate synthase (EC 2.5.1.15) | protein | 266 | 48% helix, 16% strand | D2UDM3 |
| D | Dihydropteroate synthase (EC 2.5.1.15) | protein | 261 | 48% helix, 16% strand | D2UDM3 |
Ligands and binding sites
- 6GU · 6-chloroguanine · ligand · 4 copies · chains A, C, B, D
- ICB · 1H-indole-2-carboxylic acid · ligand · 2 copies · chains A, C, D, B
- SO4 · Sulfate ion · ion · 9 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, C, B, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 820 | 0.78 | 0.82 | 83 | ICB |
| 2 | 832 | 0.77 | 0.81 | 69 | ICB, EDO |
| 3 | 192 | 0.59 | 0.81 | 30 | 6GU, SO4 |
| 4 | 151 | 0.56 | 0.82 | 30 | 6GU, SO4 |
| 5 | 103 | 0.49 | 0.81 | 24 | 6GU, SO4 |
Interfaces
5 interfaces between chains.
- A–B · 1217 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1216 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 653 Ų buried · 11 hydrogen bonds · protein-protein
- C–B · 616 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 342 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6Q62 · Xanthomonas albilineans Dihydropteroate synthase in complex with (indole-2-carboxylic… · 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 6Q62 · PDBe 6Q62 · UniProt D2UDM3
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