Research workbench
Crystal structure of the shikimate kinase + 3-dehydroquinate dehydratase + 3-dehydroshikimate dehydrogenase domains of ARO1 from candida albicans
Analyse Crystal structure of the shikimate kinase + 3-dehydroquinate dehydratase +… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TBV
- Type
- protein
- Length
- 2,719 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pentafunctional arom polypeptide
- Ligands
- MG, CL
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pentafunctional arom polypeptide | protein | 682 | 45% helix, 19% strand | — |
| B | Pentafunctional arom polypeptide | protein | 679 | 46% helix, 18% strand | — |
| C | Pentafunctional arom polypeptide | protein | 678 | 46% helix, 18% strand | — |
| D | Pentafunctional arom polypeptide | protein | 680 | 46% helix, 19% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, D
- GOL · Glycerol · additive · 13 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 855 | 0.76 | 0.80 | 82 | GOL |
| 2 | 909 | 0.76 | 0.79 | 101 | empty |
| 3 | 833 | 0.75 | 0.79 | 76 | empty |
| 4 | 671 | 0.73 | 0.80 | 55 | empty |
| 5 | 313 | 0.65 | 0.81 | 38 | empty |
Interfaces
3 interfaces between chains.
- A–B · 884 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 608 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 95 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7TBV · Crystal structure of the shikimate kinase + 3-dehydroquinate dehydratase +… · 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
- Elsewhere: RCSB PDB 7TBV · PDBe 7TBV
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