Research workbench
Crystal structure analysis of dahp synthase in complex with MN2+ and 2-phosphoglycolate
Analyse Crystal structure analysis of dahp synthase in complex with MN2+ and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GG1
- Type
- protein
- Length
- 1,361 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase
- EC
- 4.1.2.15
- UniProt
- P0AB91
- Ligands
- PGA, MN, SO4
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (EC 4.1.2.15) | protein | 339 | 39% helix, 18% strand | P0AB91 |
| B | 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (EC 4.1.2.15) | protein | 343 | 40% helix, 19% strand | P0AB91 |
| C | 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (EC 4.1.2.15) | protein | 339 | 39% helix, 19% strand | P0AB91 |
| D | 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (EC 4.1.2.15) | protein | 340 | 40% helix, 19% strand | P0AB91 |
Ligands and binding sites
- PGA · 2-phosphoglycolic acid · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1024 | 0.82 | 0.83 | 132 | empty |
| 2 | 58 | 0.72 | 0.98 | 15 | empty |
| 3 | 54 | 0.72 | 0.99 | 16 | empty |
| 4 | 56 | 0.68 | 0.96 | 19 | empty |
| 5 | 312 | 0.68 | 0.83 | 53 | PGA, SO4 |
Interfaces
6 interfaces between chains.
- A–B · 2802 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 2766 Ų buried · 46 hydrogen bonds · protein-protein
- B–D · 575 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 537 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 57 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1GG1 · Crystal structure analysis of dahp synthase in complex with MN2+ and 2-phosphoglycolate · the same entry in another collection · chain D against D, TM-score 1.00
- P0AB91 · AlphaFold monomer V2.0 prediction for phospho-2-dehydro-3-deoxyheptonate aldolase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P0AB91
- Elsewhere: RCSB PDB 1GG1 · PDBe 1GG1 · UniProt P0AB91
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