MolNFT v1 · #114724 · protein
Crystal structure of human ribokinase in P21 spacegroup
5BYD: “Crystal structure of human ribokinase in P21 spacegroup”. X-ray diffraction, 2 ligands (NA, K), 4 pockets (best druggability 0.69). MolNFT v1 #114724 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5BYD
- Type
- protein
- Length
- 627 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, K
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribokinase (EC 2.7.1.15) | protein | 315 | 38% helix, 24% strand | Q9H477 |
| B | Ribokinase (EC 2.7.1.15) | protein | 312 | 38% helix, 23% strand | Q9H477 |
Ligands and binding sites
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 | 576 | 0.69 | 0.78 | 63 | empty |
| 2 | 550 | 0.66 | 0.77 | 68 | empty |
| 3 | 127 | 0.41 | 0.75 | 29 | empty |
| 4 | 68 | 0.31 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1219 Ų buried · 12 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 5BYD · PDBe 5BYD · UniProt Q9H477
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