MolNFT v1 · #105332 · protein
Ribonucleotide reductase R1 protein with substrate, GDP and effector dttp from escherichia COLI
4R1R: “Ribonucleotide reductase R1 protein with substrate, GDP and effector dttp from escherichia COLI”. X-ray diffraction, 2 ligands (TTP, GDP), 20 pockets (best druggability 0.78). MolNFT v1 #105332 on GenesisL1: 3D structure, binding…
- 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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