MolNFT v1 · #114725 · protein
Crystal structure of human ribokinase in P212121 spacegroup
5BYE: “Crystal structure of human ribokinase in P212121 spacegroup”. X-ray diffraction, 2 ligands (NA, CL), 5 pockets (best druggability 0.71). MolNFT v1 #114725 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5BYE
- Type
- protein
- Length
- 619 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
- NA, CL
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 24% 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 | 305 | 41% helix, 24% strand | Q9H477 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 579 | 0.71 | 0.79 | 64 | empty |
| 2 | 172 | 0.41 | 0.73 | 32 | empty |
| 3 | 86 | 0.39 | 0.77 | 23 | empty |
| 4 | 100 | 0.39 | 0.76 | 22 | empty |
| 5 | 61 | 0.33 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1300 Ų buried · 13 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 5BYE · PDBe 5BYE · UniProt Q9H477
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