Research workbench
Crystal structure of prephenate dehydrogenase from a. aeolicus with hpp and NADH
Analyse Crystal structure of prephenate dehydrogenase from a. aeolicus with hpp and NADH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GGO
- Type
- protein
- Length
- 1,130 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prephenate dehydrogenase
- UniProt
- O67636
- Ligands
- NAI, ENO
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 56% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prephenate dehydrogenase | protein | 285 | 54% helix, 12% strand | O67636 |
| B | Prephenate dehydrogenase | protein | 282 | 57% helix, 12% strand | O67636 |
| C | Prephenate dehydrogenase | protein | 281 | 55% helix, 12% strand | O67636 |
| D | Prephenate dehydrogenase | protein | 282 | 56% helix, 12% strand | O67636 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- ENO · 3-(4-hydroxy-phenyl)pyruvic acid · ligand · 2 copies · chains B, D, A, C
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 | 489 | 0.75 | 0.84 | 54 | NAI |
| 2 | 438 | 0.74 | 0.84 | 61 | NAI |
| 3 | 403 | 0.74 | 0.84 | 61 | ENO, NAI |
| 4 | 475 | 0.74 | 0.83 | 64 | ENO, NAI |
| 5 | 351 | 0.56 | 0.75 | 24 | empty |
Interfaces
5 interfaces between chains.
- B–D · 4147 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 3935 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 155 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 124 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 78 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3GGO · Crystal structure of prephenate dehydrogenase from A. aeolicus with HPP and NADH · 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 3GGO · PDBe 3GGO · UniProt O67636
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