MolNFT v1 · #82519 · protein
Crystal structure of human ribonucleotide reductase subunit M2 (HRRM2) mutant
3VPM · Ribonucleoside-diphosphate reductase subunit M2: “Crystal structure of human ribonucleotide reductase subunit M2 (HRRM2) mutant”. X-ray diffraction, 2 ligands (MG, FE), 7 pockets (best druggability 0.78). MolNFT v1 #82519 on…
- PDB
- 3VPM
- Type
- protein
- Length
- 572 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase subunit M2
- EC
- 1.17.4.1
- UniProt
- P31350
- Ligands
- MG, FE
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribonucleoside-diphosphate reductase subunit M2 (EC 1.17.4.1) | protein | 286 | 71% helix, 0% strand | P31350 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.78 | 0.99 | 37 | empty |
| 2 | 132 | 0.54 | 0.81 | 21 | empty |
| 3 | 137 | 0.51 | 0.80 | 20 | empty |
| 4 | 99 | 0.49 | 0.81 | 21 | empty |
| 5 | 91 | 0.47 | 0.81 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1612 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3VPM · Crystal structure of human ribonucleotide reductase subunit M2 (hRRM2) mutant · the same entry in another collection · chain A against A, TM-score 1.00
- P31350 · AlphaFold monomer V2.0 prediction for ribonucleoside-diphosphate reductase subunit M2… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P31350
- Elsewhere: RCSB PDB 3VPM · PDBe 3VPM · UniProt P31350
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