Research workbench
Crystal structure of abbb + udp-C-gal (long soak) + di
Analyse Crystal structure of abbb + udp-C-gal (long soak) + di in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C47
- Type
- protein
- Length
- 288 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histo-blood group abo system transferase
- EC
- 2.4.1.40, 2.4.1.37
- UniProt
- P16442
- Ligands
- DA8, URM, MN
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histo-blood group abo system transferase (EC 2.4.1.40, 2.4.1.37) | protein | 288 | 33% helix, 19% strand | P16442 |
Ligands and binding sites
- DA8 · octyl 3-deoxy-2-O-(6-deoxy-alpha-L-galactopyranosyl)-beta-D-xylo-hexopyranoside · ligand · chains A
- URM · (((2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl)methyl)phosphonic (((2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl phosphoric) anhydride · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 493 | 0.64 | 0.76 | 46 | MN, DA8, URM |
| 2 | 57 | 0.33 | 0.76 | 17 | empty |
| 3 | 65 | 0.31 | 0.74 | 13 | empty |
Compared structures
- 5C47 · Crystal structure of ABBB + UDP-C-Gal (long soak) + DI · the same entry in another collection · chain A against A, TM-score 1.00
- P16442 · AlphaFold monomer V2.0 prediction for histo-blood group abo system transferase (P16442) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P16442
- Elsewhere: RCSB PDB 5C47 · PDBe 5C47 · UniProt P16442
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