MolNFT v1 · #90721 · protein
Crystal structure of a gemcitabine-diphosphate inhibited E. COLI class ia ribonucleotide reductase complex
4ERP · Ribonucleoside-diphosphate reductase 1 subunit alpha: “Crystal structure of a gemcitabine-diphosphate inhibited E. COLI class ia ribonucleotide reductase complex”. X-ray diffraction, 2 ligands (ATP, FEO), 20 pockets (best…
- PDB
- 4ERP
- Type
- protein
- Length
- 4,363 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase 1 subunit alpha; Ribonucleoside-diphosphate…
- EC
- 1.17.4.1
- UniProt
- P00452, P69924
- Ligands
- ATP, FEO
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 8 distinct chains · 51% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase 1 subunit alpha (EC 1.17.4.1) | protein | 734 | 44% helix, 10% strand | P00452 |
| B | Ribonucleoside-diphosphate reductase 1 subunit alpha (EC 1.17.4.1) | protein | 735 | 44% helix, 11% strand | P00452 |
| C | Ribonucleoside-diphosphate reductase 1 subunit alpha (EC 1.17.4.1) | protein | 733 | 45% helix, 11% strand | P00452 |
| D | Ribonucleoside-diphosphate reductase 1 subunit alpha (EC 1.17.4.1) | protein | 736 | 45% helix, 10% strand | P00452 |
| E | Ribonucleoside-diphosphate reductase 1 subunit beta (EC 1.17.4.1) | protein | 354 | 64% helix, 3% strand | P69924 |
| F | Ribonucleoside-diphosphate reductase 1 subunit beta (EC 1.17.4.1) | protein | 358 | 65% helix, 1% strand | P69924 |
| G | Ribonucleoside-diphosphate reductase 1 subunit beta (EC 1.17.4.1) | protein | 357 | 65% helix, 3% strand | P69924 |
| H | Ribonucleoside-diphosphate reductase 1 subunit beta (EC 1.17.4.1) | protein | 356 | 64% helix, 3% strand | P69924 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, D, B, C
- FEO · Mu-oxo-diiron · ligand · 4 copies · chains E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 922 | 0.84 | 0.86 | 91 | ATP |
| 2 | 439 | 0.78 | 0.86 | 61 | ATP |
| 3 | 613 | 0.78 | 0.84 | 80 | empty |
| 4 | 1058 | 0.77 | 0.79 | 93 | empty |
| 5 | 1152 | 0.77 | 0.79 | 111 | empty |
Interfaces
11 interfaces between chains.
- D–G · 1523 Ų buried · 13 hydrogen bonds · protein-protein
- B–H · 1463 Ų buried · 16 hydrogen bonds · protein-protein
- A–F · 1435 Ų buried · 8 hydrogen bonds · protein-protein
- C–E · 1349 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1331 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4ERP · Crystal structure of a gemcitabine-diphosphate inhibited E. coli class Ia ribonucleotide… · the same entry in another collection · chain H against H, TM-score 1.00
- P00452 · AlphaFold monomer V2.0 prediction for ribonucleoside-diphosphate reductase 1 subunit… · a predicted model of the same protein · chain C 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 4ERP · PDBe 4ERP · UniProt P00452 · UniProt P69924
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