Research workbench
Activation of ribokinase by monovalent cations
Analyse Activation of ribokinase by monovalent cations in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GQT
- Type
- protein
- Length
- 1,223 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribokinase
- EC
- 2.7.1.15
- UniProt
- P05054
- Ligands
- RIB, ACP, CS
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Ribokinase (EC 2.7.1.15) | protein | 305 | 39% helix, 25% strand | P05054 |
| B | Ribokinase (EC 2.7.1.15) | protein | 307 | 39% helix, 24% strand | P05054 |
| C | Ribokinase (EC 2.7.1.15) | protein | 306 | 39% helix, 25% strand | P05054 |
Ligands and binding sites
- RIB · alpha-D-ribofuranose · ligand · 4 copies · chains A, B, C, D
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 3 copies · chains A, B, C, D
- CS · Cesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 940 | 0.75 | 0.78 | 53 | empty |
| 2 | 517 | 0.74 | 0.82 | 53 | ACP, RIB |
| 3 | 582 | 0.73 | 0.81 | 56 | ACP, RIB |
| 4 | 525 | 0.72 | 0.81 | 53 | ACP, RIB |
| 5 | 506 | 0.69 | 0.80 | 49 | RIB |
Interfaces
3 interfaces between chains.
- C–D · 1129 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1118 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 461 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1GQT · Activation of Ribokinase by Monovalent Cations · 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 P05054
- Elsewhere: RCSB PDB 1GQT · PDBe 1GQT · UniProt P05054
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