MolNFT v1 · #20762 · protein
E. COLI pyruvate dehydrogenase inhibitor complex
1RP7 · Pyruvate dehydrogenase E1 component: “E. COLI pyruvate dehydrogenase inhibitor complex”. X-ray diffraction, 2 ligands (TZD, MG), 16 pockets (best druggability 0.71). MolNFT v1 #20762 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1RP7
- Type
- protein
- Length
- 1,602 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate dehydrogenase E1 component
- EC
- 1.2.4.1
- UniProt
- P06958
- Ligands
- TZD, MG
- Pockets
- 16 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyruvate dehydrogenase E1 component (EC 1.2.4.1) | protein | 801 | 44% helix, 12% strand | P06958 |
Ligands and binding sites
- TZD · 2-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-4-methyl-2-oxo-2,3-dihydro-1,3-thiazol-5-yl}ethyl trihydrogen diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.71 | 0.82 | 66 | TZD |
| 2 | 455 | 0.70 | 0.81 | 63 | MG, TZD |
| 3 | 341 | 0.69 | 0.82 | 41 | empty |
| 4 | 415 | 0.69 | 0.81 | 66 | empty |
| 5 | 194 | 0.68 | 0.86 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 5890 Ų buried · 116 hydrogen bonds · protein-protein
Compared structures
- 1RP7 · E. COLI pyruvate dehydrogenase inhibitor complex · 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 P06958
- Elsewhere: RCSB PDB 1RP7 · PDBe 1RP7 · UniProt P06958
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