MolNFT v1 · #182300 · protein
Crystal structure of the class ie ribonucleotide reductase beta-nrdi complex from aerococcus urinae in semiquinone form with CU(I) bound
7MMS · Ribonucleoside-diphosphate reductase: “Crystal structure of the class ie ribonucleotide reductase beta-nrdi complex from aerococcus urinae in…”. X-ray diffraction, 3 ligands (FNR, CU1, CA), 18 pockets (best druggability 0.76).…
- PDB
- 7MMS
- Type
- protein
- Length
- 1,773 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
- FNR, CU1, CA
- Pockets
- 18 · best druggability 0.76
Structure
x-ray diffraction · 7 distinct chains · 61% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribonucleoside-diphosphate reductase (EC 1.17.4.1) | protein | 313 | 75% helix, 1% strand | F2I8X9 |
| C | Ribonucleoside-diphosphate reductase (EC 1.17.4.1) | protein | 309 | 75% helix, 1% strand | F2I8X9 |
| D | Ribonucleoside-diphosphate reductase (EC 1.17.4.1) | protein | 320 | 75% helix, 1% strand | F2I8X9 |
| E | Protein nrdi | protein | 133 | 38% helix, 21% strand | A0A178HGH7 |
| G | Protein nrdi | protein | 129 | 36% helix, 22% strand | A0A178HGH7 |
| F | Protein nrdi | protein | 133 | 37% helix, 21% strand | A0A178HGH7 |
| H | Protein nrdi | protein | 123 | 33% helix, 23% strand | A0A178HGH7 |
Ligands and binding sites
- FNR · 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydro-2H-benzo[g]pteridin-1-id-10(5H)-yl)-5-O-phosphonato-D-ribitol · ligand · 4 copies · chains A, E, C, G, B, F, D, H
- CU1 · Copper (I) ion · metal · 4 copies · chains A, B, C
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 9 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 923 | 0.76 | 0.79 | 93 | GOL |
| 2 | 420 | 0.76 | 0.85 | 45 | FNR, GOL |
| 3 | 441 | 0.74 | 0.84 | 45 | FNR, GOL |
| 4 | 405 | 0.74 | 0.84 | 44 | FNR |
| 5 | 357 | 0.73 | 0.84 | 43 | FNR |
Interfaces
9 interfaces between chains.
- A–B · 2730 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 2723 Ų buried · 21 hydrogen bonds · protein-protein
- B–F · 1777 Ų buried · 28 hydrogen bonds · protein-protein
- A–E · 1721 Ų buried · 29 hydrogen bonds · protein-protein
- C–G · 1572 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 7MMS · 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 7MMS · PDBe 7MMS · UniProt F2I8X9 · UniProt A0A178HGH7
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