MolNFT v1 · #86619 · protein
Crystal structure of human D-xylulokinase
4BC3 · Xylulose kinase: “Crystal structure of human D-xylulokinase”. X-ray diffraction, 14 pockets (best druggability 0.76). MolNFT v1 #86619 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4BC3
- Type
- protein
- Length
- 1,577 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylulose kinase
- EC
- 2.7.1.17
- UniProt
- O75191
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xylulose kinase (EC 2.7.1.17) | protein | 525 | 42% helix, 23% strand | O75191 |
| B, C | Xylulose kinase (EC 2.7.1.17) | protein | 526 | 42% helix, 22% strand | O75191 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 781 | 0.76 | 0.80 | 61 | empty |
| 2 | 762 | 0.72 | 0.78 | 72 | empty |
| 3 | 765 | 0.70 | 0.77 | 85 | EDO |
| 4 | 550 | 0.64 | 0.76 | 52 | EDO |
| 5 | 551 | 0.64 | 0.75 | 55 | EDO |
Interfaces
3 interfaces between chains.
- A–B · 635 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 598 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 483 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
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 O75191
- Elsewhere: RCSB PDB 4BC3 · PDBe 4BC3 · UniProt O75191
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