MolNFT v1 · #115576 · protein
Crystal structure of the datp inhibited E. COLI class ia ribonucleotide reductase complex bound to GDP and ttp at 3.20 ångströms resolution
5CNV · Ribonucleoside-diphosphate reductase 1 subunit alpha: “Crystal structure of the datp inhibited E. COLI class ia ribonucleotide reductase complex bound to GDP and…”. X-ray diffraction, 5 ligands (TTP, GDP, DAT), 20 pockets (best…
- 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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