MolNFT v1 · #129475 · protein
Crystal structure of the ATP-cone-containing nrdb from leeuwenhoekiella blandensis
5OLK · Ribonucleoside-diphosphate reductase, beta subunit 1: “Crystal structure of the ATP-cone-containing nrdb from leeuwenhoekiella blandensis”. X-ray diffraction, 3 ligands (DTP, MN, MG), 13 pockets (best druggability 0.76). MolNFT v1…
- PDB
- 5OLK
- Type
- protein
- Length
- 1,574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase, beta subunit 1
- EC
- 1.17.4.1
- UniProt
- A3XHF9
- Ligands
- DTP, MN, MG
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 73% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase, beta subunit 1 (EC 1.17.4.1) | protein | 395 | 73% helix, 2% strand | A3XHF9 |
| B | Ribonucleoside-diphosphate reductase, beta subunit 1 (EC 1.17.4.1) | protein | 392 | 73% helix, 2% strand | A3XHF9 |
| C | Ribonucleoside-diphosphate reductase, beta subunit 1 (EC 1.17.4.1) | protein | 394 | 71% helix, 2% strand | A3XHF9 |
| D | Ribonucleoside-diphosphate reductase, beta subunit 1 (EC 1.17.4.1) | protein | 393 | 74% helix, 2% strand | A3XHF9 |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 8 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.76 | 0.79 | 98 | empty |
| 2 | 297 | 0.73 | 0.86 | 63 | empty |
| 3 | 606 | 0.69 | 0.78 | 53 | empty |
| 4 | 631 | 0.68 | 0.77 | 50 | empty |
| 5 | 572 | 0.67 | 0.77 | 51 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1144 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1127 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 559 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 506 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 27 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5OLK · Crystal structure of the ATP-cone-containing NrdB from Leeuwenhoekiella blandensis · 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 A3XHF9
- Elsewhere: RCSB PDB 5OLK · PDBe 5OLK · UniProt A3XHF9
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