Research workbench
Crystal structure of prephenate dehydrogenase from aquifex aeolicus
Analyse Crystal structure of prephenate dehydrogenase from aquifex aeolicus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2G5C
- Type
- protein
- Length
- 1,114 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prephenate dehydrogenase
- EC
- 1.3.1.12
- UniProt
- O67636
- Ligands
- NAD
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prephenate dehydrogenase (EC 1.3.1.12) | protein | 278 | 55% helix, 13% strand | O67636 |
| B | Prephenate dehydrogenase (EC 1.3.1.12) | protein | 280 | 58% helix, 12% strand | O67636 |
| C, D | Prephenate dehydrogenase (EC 1.3.1.12) | protein | 278 | 56% helix, 12% strand | O67636 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, 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 | 1129 | 0.82 | 0.83 | 113 | NAD |
| 2 | 687 | 0.77 | 0.82 | 70 | NAD |
| 3 | 755 | 0.77 | 0.81 | 82 | NAD |
| 4 | 447 | 0.75 | 0.84 | 58 | NAD |
| 5 | 177 | 0.56 | 0.81 | 30 | empty |
Interfaces
6 interfaces between chains.
- B–D · 3905 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 3847 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 513 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 211 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 136 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 29 modified (engineered).
Compared structures
- 2G5C · Crystal Structure of Prephenate Dehydrogenase from Aquifex aeolicus · 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 O67636
- Elsewhere: RCSB PDB 2G5C · PDBe 2G5C · UniProt O67636
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