MolNFT v1 · #37342 · protein
Catalytic domain of bovine beta 1, 4-galactosyltransferase in complex with alpha-lactalbumin, glucose, mn, and udp-N-acetylgalactosamine
2FYD: “Catalytic domain of bovine beta 1, 4-galactosyltransferase in complex with alpha-lactalbumin, glucose, mn…”. X-ray diffraction, 5 ligands (UDP, BGC, NGA), 7 pockets (best druggability 0.84). MolNFT v1 #37342 on GenesisL1: 3D…
- PDB
- 2FYD
- Type
- protein
- Length
- 790 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-lactalbumin; Beta-1,4-galactosyltransferase
- EC
- 2.4.1.-
- UniProt
- P29752
- Ligands
- UDP, BGC, NGA, CA, MN
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Alpha-lactalbumin | protein | 123 | 42% helix, 10% strand | P29752 |
| B, D | Beta-1,4-galactosyltransferase (EC 2.4.1.-) | protein | 272 | 25% helix, 22% strand | — |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains B, D
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B, C, D
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 2 copies · chains B, D
- CA · Calcium ion · metal · 2 copies · chains A, C
- MN · Manganese (II) ion · metal · 2 copies · chains B, D
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B, C, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B, C, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 700 | 0.84 | 0.88 | 77 | PG4, MES, BGC, NGA, MN, UDP |
| 2 | 681 | 0.82 | 0.86 | 71 | PG4, MES, BGC, NGA, MN, UDP |
| 3 | 489 | 0.74 | 0.83 | 65 | empty |
| 4 | 54 | 0.44 | 0.84 | 17 | empty |
| 5 | 56 | 0.43 | 0.83 | 19 | empty |
Interfaces
5 interfaces between chains.
- C–D · 661 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 648 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 368 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 207 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 60 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 2FYD · catalytic domain of bovine beta 1, 4-galactosyltransferase in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P29752 · AlphaFold monomer V2.0 prediction for alpha-lactalbumin (P29752) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P29752
- Elsewhere: RCSB PDB 2FYD · PDBe 2FYD · UniProt P29752
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