MolNFT v1 · #114726 · protein
Crystal structure of human ribokinase in complex with AMP
5BYF: “Crystal structure of human ribokinase in complex with AMP”. X-ray diffraction, 3 ligands (AMP, NA, CL), 5 pockets (best druggability 0.68). MolNFT v1 #114726 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5BYF
- Type
- protein
- Length
- 625 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
- AMP, NA, CL
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribokinase (EC 2.7.1.15) | protein | 313 | 39% helix, 23% strand | Q9H477 |
| B | Ribokinase (EC 2.7.1.15) | protein | 312 | 39% helix, 23% strand | Q9H477 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 573 | 0.68 | 0.78 | 62 | AMP, NA |
| 2 | 475 | 0.65 | 0.77 | 64 | AMP, NA |
| 3 | 73 | 0.37 | 0.77 | 16 | empty |
| 4 | 65 | 0.32 | 0.75 | 15 | empty |
| 5 | 56 | 0.30 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1309 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
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 5BYF · PDBe 5BYF · UniProt Q9H477
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