MolNFT v1 · #140625 · protein
Crystal structure of escherichia COLI (strain K12) mRNA decapping complex rpph-dapf
5YGU · Diaminopimelate epimerase: “Crystal structure of escherichia COLI (strain K12) mRNA decapping complex rpph-dapf”. X-ray diffraction, 1 ligand (IOD), 6 pockets (best druggability 0.65). MolNFT v1 #140625 on GenesisL1: 3D structure…
- PDB
- 5YGU
- Type
- protein
- Length
- 424 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diaminopimelate epimerase; RNA pyrophosphohydrolase
- EC
- 5.1.1.7, 3.6.1.-
- UniProt
- P0A6K1, P0A776
- Ligands
- IOD
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diaminopimelate epimerase (EC 5.1.1.7) | protein | 274 | 16% helix, 40% strand | P0A6K1 |
| B | RNA pyrophosphohydrolase (EC 3.6.1.-) | protein | 150 | 29% helix, 30% strand | P0A776 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.65 | 0.83 | 35 | TLA, IOD |
| 2 | 92 | 0.57 | 0.86 | 22 | empty |
| 3 | 91 | 0.48 | 0.82 | 19 | empty |
| 4 | 65 | 0.46 | 0.83 | 17 | IOD |
| 5 | 94 | 0.35 | 0.74 | 18 | IOD |
Interfaces
1 interface between chains.
- A–B · 663 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5YGU · Crystal structure of Escherichia coli (strain K12) mRNA Decapping Complex RppH-DapF · the same entry in another collection · chain A against A, TM-score 1.00
- P0A6K1 · AlphaFold monomer V2.0 prediction for diaminopimelate epimerase (P0A6K1) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P0A776 · AlphaFold monomer V2.0 prediction for RNA pyrophosphohydrolase (P0A776) · a predicted model of the same protein · chain B 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 P0A6K1
- Every structure of UniProt P0A776
- Elsewhere: RCSB PDB 5YGU · PDBe 5YGU · UniProt P0A6K1 · UniProt P0A776
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