Research workbench
Crystal structure of BETA14,-galactosyltransferase mutant ARG228LYS in complex with alpha-lactalbumin in the presence of udp-galactose and mn
Analyse Crystal structure of BETA14,-galactosyltransferase mutant ARG228LYS in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YRO
- 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
- 2.4.1.22, 2.4.1.90, 2.4.1.38
- UniProt
- P29752, P08037
- Ligands
- GDU, UDP, CA, MN
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Alpha-lactalbumin | protein | 123 | 42% helix, 11% strand | P29752 |
| B, D | Beta-1,4-galactosyltransferase (EC 2.4.1.22, 2.4.1.90, 2.4.1.38) | protein | 272 | 26% helix, 22% strand | P08037 |
Ligands and binding sites
- GDU · Galactose-uridine-5'-diphosphate · ligand · 2 copies · chains B, D
- UDP · Uridine-5'-diphosphate · ligand · 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 · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 929 | 0.85 | 0.87 | 113 | PG4, GDU, MN |
| 2 | 719 | 0.80 | 0.84 | 70 | MES, PG4, GDU, MN |
| 3 | 242 | 0.63 | 0.81 | 25 | empty |
| 4 | 53 | 0.45 | 0.84 | 18 | empty |
| 5 | 90 | 0.43 | 0.79 | 15 | empty |
Interfaces
5 interfaces between chains.
- C–D · 722 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 650 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 352 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 273 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 67 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 1YRO · Crystal structure of beta14,-galactosyltransferase mutant ARG228Lys in complex with… · the same entry in another collection · chain B against B, 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 0.94
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
- Every structure of UniProt P08037
- Elsewhere: RCSB PDB 1YRO · PDBe 1YRO · UniProt P29752 · UniProt P08037
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