Research workbench
Crystal structure of truncated (act domain removed) prephenate dehydrogenase tyra from bacillus anthracis in complex with NAD
Analyse Crystal structure of truncated (act domain removed) prephenate dehydrogenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MQV
- Type
- protein
- Length
- 1,160 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prephenate dehydrogenase
- EC
- 1.3.1.12
- UniProt
- Q81P63
- Ligands
- NAD, CL
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prephenate dehydrogenase (EC 1.3.1.12) | protein | 294 | 58% helix, 13% strand | Q81P63 |
| B | Prephenate dehydrogenase (EC 1.3.1.12) | protein | 286 | 57% helix, 14% strand | Q81P63 |
| C | Prephenate dehydrogenase (EC 1.3.1.12) | protein | 292 | 57% helix, 13% strand | Q81P63 |
| D | Prephenate dehydrogenase (EC 1.3.1.12) | protein | 288 | 58% helix, 14% strand | Q81P63 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains D
- GOL · Glycerol · additive · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 557 | 0.79 | 0.85 | 62 | NAD |
| 2 | 536 | 0.78 | 0.84 | 57 | NAD |
| 3 | 907 | 0.77 | 0.80 | 93 | NAD |
| 4 | 599 | 0.76 | 0.83 | 52 | NAD, GOL |
| 5 | 111 | 0.44 | 0.78 | 20 | empty |
Interfaces
6 interfaces between chains.
- C–D · 4686 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 4573 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 732 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 307 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 280 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7MQV · Crystal structure of truncated (ACT domain removed) prephenate dehydrogenase tyrA from… · 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 Q81P63
- Elsewhere: RCSB PDB 7MQV · PDBe 7MQV · UniProt Q81P63
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