Research workbench
Crystal structure of the cofactor-binding domain of the human phase II drug metabolism enzyme UGT2B15
Analyse Crystal structure of the cofactor-binding domain of the human phase II drug… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IPB
- Type
- protein
- Length
- 680 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-glucuronosyltransferase 2B15
- EC
- 2.4.1.17
- UniProt
- P54855
- Pockets
- 7 · best druggability 0.44
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-glucuronosyltransferase 2B15 (EC 2.4.1.17) | protein | 171 | 46% helix, 15% strand | P54855 |
| B, C | Udp-glucuronosyltransferase 2B15 (EC 2.4.1.17) | protein | 170 | 44% helix, 15% strand | P54855 |
| D | Udp-glucuronosyltransferase 2B15 (EC 2.4.1.17) | protein | 169 | 44% helix, 15% strand | P54855 |
Ligands and binding sites
- TLA · L(+)-tartaric acid · additive · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.44 | 0.75 | 29 | empty |
| 2 | 166 | 0.42 | 0.74 | 29 | empty |
| 3 | 91 | 0.34 | 0.74 | 20 | empty |
| 4 | 60 | 0.31 | 0.75 | 16 | empty |
| 5 | 56 | 0.29 | 0.74 | 12 | empty |
Interfaces
4 interfaces between chains.
- B–D · 286 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 274 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 210 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 12 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6IPB · Crystal Structure of the Cofactor-binding Domain of the Human Phase II Drug Metabolism… · the same entry in another collection · chain A against A, TM-score 1.00
- P54855 · AlphaFold monomer V2.0 prediction for udp-glucuronosyltransferase 2B15 (P54855) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P54855
- Elsewhere: RCSB PDB 6IPB · PDBe 6IPB · UniProt P54855
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