Research workbench
Crystal structure of human ribokinase in complex with amppcp in P21 spacegroup
Analyse Crystal structure of human ribokinase in complex with amppcp in P21 spacegroup in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C40
- Type
- protein
- Length
- 626 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribokinase
- EC
- 2.7.1.15
- UniProt
- Q9H477
- Ligands
- ACP, NA, PO4
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribokinase (EC 2.7.1.15) | protein | 314 | 39% helix, 23% strand | Q9H477 |
| B | Ribokinase (EC 2.7.1.15) | protein | 312 | 38% helix, 23% strand | Q9H477 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 3 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 | 535 | 0.67 | 0.78 | 59 | ACP, NA |
| 2 | 503 | 0.67 | 0.78 | 60 | ACP, NA |
| 3 | 89 | 0.38 | 0.76 | 18 | empty |
| 4 | 61 | 0.31 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1245 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5C40 · Crystal structure of human ribokinase in complex with AMPPCP in P21 spacegroup · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H477 · AlphaFold monomer V2.0 prediction for ribokinase (Q9H477) · 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 Q9H477
- Elsewhere: RCSB PDB 5C40 · PDBe 5C40 · UniProt Q9H477
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