MolNFT v1 · #48497 · protein
Crystal structure of chorismate mutase / prephenate dehydrogenase (tyra) (1574749) from haemophilus influenzae rd at 2.00 a resolution
2PV7 · T-protein [includes: chorismate mutase (ec 5.4.99.5) (cm)…: “Crystal structure of chorismate mutase / prephenate dehydrogenase (tyra) (1574749) from haemophilus…”. X-ray diffraction, 2 ligands (TYR, NAD), 5 pockets (best…
- PDB
- 2PV7
- Type
- protein
- Length
- 556 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-protein [includes: chorismate mutase (ec 5.4.99.5) (cm) and prephenate dehydrogenase…
- EC
- 5.4.99.5, 1.3.1.12
- UniProt
- P43902
- Ligands
- TYR, NAD
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-protein [includes: chorismate mutase (ec 5.4.99.5) (cm) and prephenate dehydrogenase (ec 1.3.1.12) (pdh)] (EC 5.4.99.5, 1.3.1.12) | protein | 276 | 57% helix, 13% strand | P43902 |
| B | T-protein [includes: chorismate mutase (ec 5.4.99.5) (cm) and prephenate dehydrogenase (ec 1.3.1.12) (pdh)] (EC 5.4.99.5, 1.3.1.12) | protein | 280 | 58% helix, 13% strand | P43902 |
Ligands and binding sites
- TYR · Tyrosine · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 461 | 0.77 | 0.85 | 58 | TYR, NAD |
| 2 | 576 | 0.76 | 0.83 | 76 | TYR, NAD |
| 3 | 80 | 0.76 | 0.99 | 14 | empty |
| 4 | 75 | 0.37 | 0.77 | 19 | empty |
| 5 | 89 | 0.37 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 5638 Ų buried · 50 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 2PV7 · Crystal structure of chorismate mutase / prephenate dehydrogenase (tyrA) (1574749) from… · the same entry in another collection · chain B against B, TM-score 1.00
- P43902 · AlphaFold monomer V2.0 prediction for T-protein (P43902) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P43902
- Elsewhere: RCSB PDB 2PV7 · PDBe 2PV7 · UniProt P43902
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