Research workbench
Structure of rbkr (riboflavin kinase) from thermoplasma acidophilum determined in complex with CTP and its cognate DNA operator
Analyse Structure of rbkr (riboflavin kinase) from thermoplasma acidophilum determined… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TRD
- Type
- protein + DNA
- Length
- 472 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Riboflavin kinase; DNA (5'- D(*AP*TP*TP*AP*CP*TP*AP*AP*TP*TP*CP*AP*CP*GP*AP*GP*TP*AP*A)-3'…
- EC
- 2.7.1.161
- UniProt
- Q9HJA6
- Ligands
- CTP, NA
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Riboflavin kinase (EC 2.7.1.161) | protein | 219 | 39% helix, 29% strand | Q9HJA6 |
| B | Riboflavin kinase (EC 2.7.1.161) | protein | 215 | 38% helix, 29% strand | Q9HJA6 |
| G | DNA (5'- D(*AP*TP*TP*AP*CP*TP*AP*AP*TP*TP*CP*AP*CP*GP*AP*GP*TP*AP*A)-3') | dna | 19 | — | — |
| H | DNA (5'- D(P*TP*TP*TP*AP*CP*TP*CP*GP*TP*GP*AP*AP*TP*TP*AP*GP*TP*AP*A)-3') | dna | 19 | — | — |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 348 | 0.64 | 0.79 | 42 | CTP, NA |
| 2 | 290 | 0.63 | 0.80 | 41 | CTP, NA |
| 3 | 142 | 0.42 | 0.75 | 22 | empty |
| 4 | 110 | 0.37 | 0.75 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 990 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 821 Ų buried · 81 hydrogen bonds · nucleic-nucleic
- B–G · 442 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–H · 394 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–G · 247 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 5TRD · Structure of RbkR (Riboflavin Kinase) from Thermoplasma acidophilum determined in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HJA6 · AlphaFold monomer V2.0 prediction for riboflavin kinase (Q9HJA6) · a predicted model of the same protein · chain B 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 Q9HJA6
- Elsewhere: RCSB PDB 5TRD · PDBe 5TRD · UniProt Q9HJA6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.