Research workbench
Blood group synthase aaglyb in complex with udp and cryoprotected with peg 3350
Analyse Blood group synthase aaglyb in complex with udp and cryoprotected with peg 3350 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M7C
- Type
- protein
- Length
- 586 residues
- Chains
- 2
- 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
- UDP, MN, SO4
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Histo-blood group abo system transferase (EC 2.4.1.40, 2.4.1.37) | protein | 293 | 34% helix, 18% strand | P16442 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 477 | 0.75 | 0.84 | 44 | MN, UDP |
| 2 | 839 | 0.75 | 0.79 | 62 | empty |
| 3 | 463 | 0.73 | 0.82 | 41 | MN, UDP |
| 4 | 70 | 0.34 | 0.76 | 11 | empty |
| 5 | 69 | 0.33 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2506 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 5M7C · Blood group synthase AAGlyB in complex with UDP and cryoprotected with PEG 3350 · 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 B against A, TM-score 1.00
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 5M7C · PDBe 5M7C · UniProt P16442
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.