Research workbench
Ribonucleotide reductase R1 protein with substrate, GDP and effector dttp from escherichia COLI
Analyse Ribonucleotide reductase R1 protein with substrate, GDP and effector dttp from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R1R
- Type
- protein
- Length
- 2,250 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleotide reductase R1 protein; Ribonucleotide reductase R2 protein
- EC
- 1.17.4.1
- UniProt
- P00452, P69924
- Ligands
- TTP, GDP
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Ribonucleotide reductase R1 protein (EC 1.17.4.1) | protein | 733 | 48% helix, 13% strand | P00452 |
| D, E, F | Ribonucleotide reductase R2 protein | protein | 16 | 25% helix, 13% strand | P69924 |
| P | Ribonucleotide reductase R2 protein | protein | 3 | 0% helix, 0% strand | P69924 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 3 copies · chains A, B, C
- GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1183 | 0.78 | 0.80 | 108 | GDP, TTP |
| 2 | 1134 | 0.78 | 0.80 | 104 | TTP, GDP |
| 3 | 776 | 0.72 | 0.78 | 81 | GDP |
| 4 | 156 | 0.71 | 0.90 | 31 | empty |
| 5 | 145 | 0.56 | 0.81 | 19 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1482 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 906 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 906 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 902 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 283 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4R1R · Ribonucleotide reductase R1 protein with substrate, GDP and effector dttp from… · the same entry in another collection · chain P against P, TM-score 1.00
- P00452 · AlphaFold monomer V2.0 prediction for ribonucleoside-diphosphate reductase 1 subunit… · 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 P00452
- Every structure of UniProt P69924
- Elsewhere: RCSB PDB 4R1R · PDBe 4R1R · UniProt P00452 · UniProt P69924
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