MolNFT v1 · #64890 · protein
Crystal structure of prephenate dehydrogenase from a. aeolicus with hpp and NADH
3GGO: “Crystal structure of prephenate dehydrogenase from a. aeolicus with hpp and NADH”. X-ray diffraction, 2 ligands (NAI, ENO), 8 pockets (best druggability 0.75). MolNFT v1 #64890 on GenesisL1: 3D structure, binding sites and pockets…
- 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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