MolNFT v1 · #37341 · protein
Crystal structure of the catalytic domain of bovine BETA1,4- galactosyltransferase-I in complex with alpha-lactalbumin, ca and udp-galactose
2FYC: “Crystal structure of the catalytic domain of bovine BETA1,4- galactosyltransferase-I in complex with…”. X-ray diffraction, 3 ligands (GDU, UDP, CA), 6 pockets (best druggability 0.84). MolNFT v1 #37341 on GenesisL1: 3D structure…
- PDB
- 2FYC
- 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, P08037
- Ligands
- GDU, UDP, CA
- Pockets
- 6 · best druggability 0.84
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.-) | 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 · 4 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
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 | 606 | 0.84 | 0.89 | 68 | GDU, CA |
| 2 | 494 | 0.82 | 0.89 | 55 | MES, GDU, CA |
| 3 | 337 | 0.74 | 0.85 | 58 | empty |
| 4 | 57 | 0.41 | 0.81 | 20 | empty |
| 5 | 60 | 0.35 | 0.78 | 13 | empty |
Interfaces
5 interfaces between chains.
- C–D · 682 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 634 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 364 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 247 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 76 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 2FYC · Crystal structure of the catalytic domain of bovine beta1,4-galactosyltransferase-I in… · 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 0.94
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 2FYC · PDBe 2FYC · UniProt P29752 · UniProt P08037
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