MolNFT v1 · #182439 · protein
Crystal structure of truncated (act domain removed) prephenate dehydrogenase tyra from bacillus anthracis in complex with NAD
7MQV: “Crystal structure of truncated (act domain removed) prephenate dehydrogenase tyra from bacillus anthracis in…”. X-ray diffraction, 2 ligands (NAD, CL), 8 pockets (best druggability 0.79). MolNFT v1 #182439 on GenesisL1: 3D…
- 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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