Research workbench
Crystal structure of the datp inhibited E. COLI class ia ribonucleotide reductase complex bound to GDP and ttp at 3.20 ångströms resolution
Analyse Crystal structure of the datp inhibited E. COLI class ia ribonucleotide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CNV
- Type
- protein
- Length
- 4,361 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
- TTP, GDP, DAT, FEO, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase 1 subunit alpha (EC 1.17.4.1) | protein | 736 | 45% helix, 13% strand | P00452 |
| B | Ribonucleoside-diphosphate reductase 1 subunit alpha (EC 1.17.4.1) | protein | 732 | 45% helix, 13% strand | P00452 |
| C, D | Ribonucleoside-diphosphate reductase 1 subunit alpha (EC 1.17.4.1) | protein | 734 | 46% helix, 13% strand | P00452 |
| E | Ribonucleoside-diphosphate reductase 1 subunit beta (EC 1.17.4.1) | protein | 352 | 68% helix, 4% strand | P69924 |
| F, G | Ribonucleoside-diphosphate reductase 1 subunit beta (EC 1.17.4.1) | protein | 357 | 68% helix, 4% strand | P69924 |
| H | Ribonucleoside-diphosphate reductase 1 subunit beta (EC 1.17.4.1) | protein | 359 | 67% helix, 4% strand | P69924 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 8 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- DAT · 2'-deoxyadenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- FEO · Mu-oxo-diiron · ligand · 4 copies · chains E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 648 | 0.81 | 0.86 | 104 | TTP, GDP |
| 2 | 558 | 0.79 | 0.85 | 81 | TTP, GDP |
| 3 | 569 | 0.78 | 0.85 | 80 | GDP, TTP |
| 4 | 236 | 0.75 | 0.89 | 41 | TTP |
| 5 | 104 | 0.74 | 0.95 | 26 | empty |
Interfaces
8 interfaces between chains.
- E–H · 3222 Ų buried · 54 hydrogen bonds · protein-protein
- F–G · 3215 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 1783 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1769 Ų buried · 21 hydrogen bonds · protein-protein
- A–G · 1560 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 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 0.98
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 5CNV · PDBe 5CNV · UniProt P00452 · UniProt P69924
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