MolNFT v1 · #86618 · protein
Crystal structure of human D-xylulokinase in complex with D-xylulose and adenosine diphosphate
4BC2 · Xylulose kinase: “Crystal structure of human D-xylulokinase in complex with D-xylulose and adenosine diphosphate”. X-ray diffraction, 2 ligands (ADP, XUL), 13 pockets (best druggability 0.75). MolNFT v1 #86618 on GenesisL1: 3D…
- PDB
- 4BC2
- Type
- protein
- Length
- 1,582 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
- Ligands
- ADP, XUL
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xylulose kinase (EC 2.7.1.17) | protein | 528 | 41% helix, 22% strand | O75191 |
| B, C | Xylulose kinase (EC 2.7.1.17) | protein | 527 | 42% helix, 22% strand | O75191 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- XUL · D-xylulose · ligand · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.75 | 0.78 | 81 | empty |
| 2 | 791 | 0.72 | 0.78 | 78 | ADP |
| 3 | 834 | 0.71 | 0.76 | 67 | empty |
| 4 | 570 | 0.65 | 0.76 | 60 | XUL |
| 5 | 484 | 0.63 | 0.76 | 48 | XUL |
Interfaces
3 interfaces between chains.
- B–C · 557 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 391 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 344 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 4BC2 · Crystal structure of human D-xylulokinase in complex with D-xylulose and adenosine… · the same entry in another collection · chain A against A, TM-score 1.00
- O75191 · AlphaFold monomer V2.0 prediction for xylulose kinase (O75191) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 4BC2 · PDBe 4BC2 · UniProt O75191
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