Research workbench
W314A-BETA1,4-galactosyltransferase-I complexed with alpha-lactalbumin in the presence of N-acetylglucosamine, udp and manganese
Analyse W314A-BETA1,4-galactosyltransferase-I complexed with alpha-lactalbumin in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PZY
- Type
- protein
- Length
- 788 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Bos taurus; Mus musculus
- Molecule
- Alpha-lactalbumin; Beta-1,4-galactosyltransferase
- EC
- 2.4.1.22, 2.4.1.90, 2.4.1.38
- UniProt
- P29752, P08037
- Ligands
- UDP, NAG, CA, MN
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.3 · 2 distinct chains · 31% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Alpha-lactalbumin | protein | 123 | 42% helix, 8% strand | P29752 |
| B, D | Beta-1,4-galactosyltransferase (EC 2.4.1.22, 2.4.1.90, 2.4.1.38) | protein | 271 | 27% helix, 23% strand | P08037 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains B, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains A, C
- MN · Manganese (II) ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 998 | 0.83 | 0.84 | 79 | NAG, MN, UDP |
| 2 | 924 | 0.81 | 0.83 | 74 | NAG, MN, UDP |
| 3 | 59 | 0.43 | 0.82 | 21 | empty |
| 4 | 68 | 0.36 | 0.77 | 18 | empty |
| 5 | 51 | 0.30 | 0.76 | 14 | empty |
Interfaces
2 interfaces between chains.
- C–D · 657 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 622 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 1PZY · W314A-BETA1,4-galactosyltransferase-I complexed with alpha-lactalbumin in the presence of… · the same entry in another collection · chain A against A, TM-score 1.00
- P08037 · AlphaFold monomer V2.0 prediction for beta-1,4-galactosyltransferase 1 (P08037) · a predicted model of the same protein · chain B 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 0.95
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
- Every structure of UniProt P08037
- Elsewhere: RCSB PDB 1PZY · PDBe 1PZY · UniProt P29752 · UniProt P08037
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