MolNFT v1 · #64891 · protein
Crystal structure of prephenate dehydrogenase from a. aeolicus in complex with hydroxyphenyl propionate and NAD+
3GGP: “Crystal structure of prephenate dehydrogenase from a. aeolicus in complex with hydroxyphenyl propionate and…”. X-ray diffraction, 3 ligands (NAD, HPP, CL), 5 pockets (best druggability 0.76). MolNFT v1 #64891 on GenesisL1: 3D…
- PDB
- 3GGP
- Type
- protein
- Length
- 1,142 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prephenate dehydrogenase
- UniProt
- O67636
- Ligands
- NAD, HPP, CL
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Prephenate dehydrogenase | protein | 286 | 56% helix, 12% strand | O67636 |
| B | Prephenate dehydrogenase | protein | 284 | 56% helix, 12% strand | O67636 |
| C | Prephenate dehydrogenase | protein | 286 | 56% helix, 13% strand | O67636 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- HPP · Hydroxyphenyl propionic acid · ligand · 2 copies · chains B, D, A, C
- CL · Chloride ion · ion · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.76 | 0.85 | 56 | NAD |
| 2 | 525 | 0.76 | 0.83 | 59 | NAD |
| 3 | 860 | 0.75 | 0.79 | 98 | CL, NAD, HPP |
| 4 | 391 | 0.74 | 0.84 | 59 | NAD, HPP |
| 5 | 51 | 0.27 | 0.74 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–C · 4244 Ų buried · 49 hydrogen bonds · protein-protein
- B–D · 4232 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 120 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 111 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 78 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3GGP · Crystal structure of prephenate dehydrogenase from A. aeolicus in complex with… · the same entry in another collection · chain C against C, 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 3GGP · PDBe 3GGP · UniProt O67636
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