MolNFT v1 · #145913 · protein + RNA
Crystal structure of E. COLI rpph-dapf complex, monomer bound to RNA
6D1V · Diaminopimelate epimerase: “Crystal structure of E. COLI rpph-dapf complex, monomer bound to RNA”. X-ray diffraction, 2 ligands (MG, CL), 3 pockets (best druggability 0.57). MolNFT v1 #145913 on GenesisL1: 3D structure, binding…
- PDB
- 6D1V
- Type
- protein + RNA
- Length
- 436 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diaminopimelate epimerase; RNA pyrophosphohydrolase; RNA (5'-D(*(APC))-R(P*GP*U)-3')
- EC
- 3.6.1.-
- UniProt
- P0A6K1, P0A776
- Ligands
- MG, CL
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diaminopimelate epimerase | protein | 275 | 15% helix, 40% strand | P0A6K1 |
| B | RNA pyrophosphohydrolase (EC 3.6.1.-) | protein | 159 | 29% helix, 31% strand | P0A776 |
| C | RNA (5'-D(*(APC))-R(P*GP*U)-3') | rna | 2 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains B, C
- CL · Chloride ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.57 | 0.77 | 38 | CL |
| 2 | 85 | 0.35 | 0.75 | 15 | CL |
| 3 | 69 | 0.34 | 0.76 | 20 | empty |
Interfaces
2 interfaces between chains.
- A–B · 751 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 497 Ų buried · 19 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6D1V · Crystal structure of E. coli RppH-DapF complex, monomer bound to RNA · the same entry in another collection · chain A against A, TM-score 1.00
- P0A776 · AlphaFold monomer V2.0 prediction for RNA pyrophosphohydrolase (P0A776) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P0A6K1 · AlphaFold monomer V2.0 prediction for diaminopimelate epimerase (P0A6K1) · a predicted model of the same protein · chain A against A, TM-score 0.89
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 6D1V · PDBe 6D1V · UniProt P0A6K1 · UniProt P0A776
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