Research workbench
The crystal structure of a. aeolicus prephenate dehydrogenase in complex with tyrosine and NAD+
Analyse The crystal structure of a. aeolicus prephenate dehydrogenase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GGG
- Type
- protein
- Length
- 1,149 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prephenate dehydrogenase
- UniProt
- O67636
- Ligands
- NAD, TYR
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Prephenate dehydrogenase | protein | 293 | 57% helix, 12% strand | O67636 |
| A | Prephenate dehydrogenase | protein | 285 | 58% helix, 12% strand | O67636 |
| B | Prephenate dehydrogenase | protein | 290 | 56% helix, 12% strand | O67636 |
| C | Prephenate dehydrogenase | protein | 281 | 57% helix, 12% strand | O67636 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains D, A, B, C
- TYR · Tyrosine · ligand · 2 copies · chains D, B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 786 | 0.78 | 0.82 | 69 | NAD |
| 2 | 553 | 0.78 | 0.84 | 60 | NAD |
| 3 | 385 | 0.76 | 0.86 | 51 | NAD, TYR |
| 4 | 439 | 0.75 | 0.84 | 61 | NAD, TYR |
| 5 | 675 | 0.64 | 0.74 | 69 | empty |
Interfaces
5 interfaces between chains.
- D–B · 4149 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 3862 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 237 Ų buried · 4 hydrogen bonds · protein-protein
- D–A · 169 Ų buried · 3 hydrogen bonds · protein-protein
- D–C · 147 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3GGG · The crystal structure of A. aeolicus prephenate dehydrogenase in complex with tyrosine… · the same entry in another collection · chain B against B, 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 3GGG · PDBe 3GGG · UniProt O67636
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