MolNFT v1 · #18349 · protein
Crystal structure of manganese substituted R2-D84E (D84E mutant of the R2 subunit of E. COLI ribonucleotide reductase)
1PM2 · Ribonucleoside-diphosphate reductase 1 beta chain: “Crystal structure of manganese substituted R2-D84E (D84E mutant of the R2 subunit of E. COLI ribonucleotide…”. X-ray diffraction, 2 ligands (HG, MN), 2 pockets (best druggability…
- PDB
- 1PM2
- Type
- protein
- Length
- 678 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase 1 beta chain
- EC
- 1.17.4.1
- UniProt
- P69924
- Ligands
- HG, MN
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribonucleoside-diphosphate reductase 1 beta chain (EC 1.17.4.1) | protein | 339 | 69% helix, 4% strand | P69924 |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 14 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.75 | 0.94 | 28 | empty |
| 2 | 80 | 0.51 | 0.84 | 16 | HG |
Interfaces
1 interface between chains.
- A–B · 3075 Ų buried · 50 hydrogen bonds · protein-protein
Compared structures
- 1PM2 · Crystal structure of manganese substituted R2-D84E (D84E mutant of the R2 subunit of E.… · the same entry in another collection · chain B against B, 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 P69924
- Elsewhere: RCSB PDB 1PM2 · PDBe 1PM2 · UniProt P69924
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