MolNFT v1 · #95485 · protein
Crystal structure of catalytic domain of human BETA1,4- galactosyltransferase-7 in open conformation with manganses and udp
4IRP · Beta-1,4-galactosyltransferase 7: “Crystal structure of catalytic domain of human BETA1,4- galactosyltransferase-7 in open conformation with…”. X-ray diffraction, 2 ligands (UDP, MN), 5 pockets (best druggability 0.56). MolNFT v1…
- PDB
- 4IRP
- Type
- protein
- Length
- 459 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-1,4-galactosyltransferase 7
- EC
- 2.4.1.-, 2.4.1.133
- UniProt
- Q9UBV7
- Ligands
- UDP, MN
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-1,4-galactosyltransferase 7 (EC 2.4.1.-, 2.4.1.133) | protein | 232 | 24% helix, 24% strand | Q9UBV7 |
| B | Beta-1,4-galactosyltransferase 7 (EC 2.4.1.-, 2.4.1.133) | protein | 227 | 24% helix, 25% strand | Q9UBV7 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 6 copies · chains A, B
- IMD · Imidazole · additive · chains A
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 | 276 | 0.56 | 0.77 | 26 | UDP, MN |
| 2 | 228 | 0.50 | 0.75 | 26 | UDP, MN |
| 3 | 83 | 0.49 | 0.83 | 18 | empty |
| 4 | 84 | 0.40 | 0.78 | 14 | empty |
| 5 | 73 | 0.37 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 794 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4IRP · Crystal structure of catalytic domain of human beta1,4-galactosyltransferase-7 in open… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UBV7 · AlphaFold monomer V2.0 prediction for beta-1,4-galactosyltransferase 7 (Q9UBV7) · a predicted model of the same protein · chain B 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 Q9UBV7
- Elsewhere: RCSB PDB 4IRP · PDBe 4IRP · UniProt Q9UBV7
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