MolNFT v1 · #114893 · protein
Crystal structure of abbb + udp-C-gal (short soak) + di
5C3D · Histo-blood group abo system transferase: “Crystal structure of abbb + udp-C-gal (short soak) + di”. X-ray diffraction, 2 ligands (URM, MN), 4 pockets (best druggability 0.50). MolNFT v1 #114893 on GenesisL1: 3D structure, binding…
- PDB
- 5C3D
- Type
- protein
- Length
- 278 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
- URM, MN
- Pockets
- 4 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 20% 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 | 278 | 32% helix, 20% strand | P16442 |
Ligands and binding sites
- 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
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.50 | 0.75 | 19 | URM |
| 2 | 74 | 0.31 | 0.73 | 14 | empty |
| 3 | 53 | 0.31 | 0.76 | 17 | empty |
| 4 | 52 | 0.30 | 0.76 | 14 | MN |
Compared structures
- 5C3D · Crystal structure of ABBB + UDP-C-Gal (short 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 0.99
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 P16442
- Elsewhere: RCSB PDB 5C3D · PDBe 5C3D · UniProt P16442
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