Research workbench
Crystal structure of the class ie ribonucleotide reductase beta-nrdi complex from aerococcus urinae in oxidized form with CU(I) bound
Analyse Crystal structure of the class ie ribonucleotide reductase beta-nrdi complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MMR
- Type
- protein
- Length
- 1,782 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase; Protein nrdi
- EC
- 1.17.4.1
- UniProt
- F2I8X9, A0A178HGH7
- Ligands
- FMN, CU1, CA
- Pockets
- 19 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 59% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Ribonucleoside-diphosphate reductase (EC 1.17.4.1) | protein | 309 | 75% helix, 1% strand | F2I8X9 |
| B | Ribonucleoside-diphosphate reductase (EC 1.17.4.1) | protein | 311 | 74% helix, 1% strand | F2I8X9 |
| E, H | Protein nrdi | protein | 136 | 37% helix, 22% strand | A0A178HGH7 |
| G | Protein nrdi | protein | 134 | 36% helix, 22% strand | A0A178HGH7 |
| F | Protein nrdi | protein | 138 | 36% helix, 22% strand | A0A178HGH7 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, E, C, G, B, F, D, H
- CU1 · Copper (I) ion · metal · 9 copies · chains A, B, C, D
- CA · Calcium ion · metal · 7 copies · chains C, D, A, E, G, B, F, H
- GOL · Glycerol · additive · 6 copies · chains A, E, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 445 | 0.75 | 0.84 | 47 | FMN, CA |
| 2 | 764 | 0.75 | 0.80 | 75 | empty |
| 3 | 431 | 0.75 | 0.84 | 49 | GOL, FMN, CA |
| 4 | 455 | 0.74 | 0.84 | 47 | FMN, CA |
| 5 | 428 | 0.74 | 0.84 | 46 | FMN, CA |
Interfaces
9 interfaces between chains.
- A–B · 2772 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 2752 Ų buried · 20 hydrogen bonds · protein-protein
- A–E · 1675 Ų buried · 33 hydrogen bonds · protein-protein
- B–F · 1640 Ų buried · 25 hydrogen bonds · protein-protein
- D–H · 1603 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 7MMR · Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-NrdI complex from… · the same entry in another collection · chain A against A, TM-score 1.00
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 F2I8X9
- Every structure of UniProt A0A178HGH7
- Elsewhere: RCSB PDB 7MMR · PDBe 7MMR · UniProt F2I8X9 · UniProt A0A178HGH7
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