Research workbench
Crystal structure of human M340H-beta-1,4-galactosyltransferase- I(M340H-B4GAL-T1) in complex with glcnac-BETA1,4-man-ALPHA1,3-man- beta-or
Analyse Crystal structure of human M340H-beta-1,4-galactosyltransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AGD
- Type
- protein
- Length
- 819 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-1,4-galactosyltransferase 1
- EC
- 2.4.1.90
- UniProt
- P15291
- Ligands
- UDH, BMA, MAN, NAG, MN, SO4
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Beta-1,4-galactosyltransferase 1 (EC 2.4.1.90) | protein | 273 | 26% helix, 22% strand | P15291 |
Ligands and binding sites
- UDH · 6-aminohexyl-uridine-C1,5'-diphosphate · ligand · 3 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B, C
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 16 copies · chains A, B, C
- GOL · Glycerol · additive · 8 copies · chains A, B, C
- DIO · 1,4-diethylene dioxide · additive · chains C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 404 | 0.72 | 0.83 | 40 | SO4 |
| 2 | 331 | 0.72 | 0.84 | 40 | NAG, MN, UDH, GOL |
| 3 | 358 | 0.72 | 0.84 | 41 | NAG, UDH, GOL |
| 4 | 332 | 0.70 | 0.83 | 39 | NAG, MN, UDH, GOL |
| 5 | 418 | 0.64 | 0.78 | 51 | SO4, GOL |
Interfaces
2 interfaces between chains.
- A–B · 628 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 536 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2AGD · Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-I(M340H-B4Gal-T1) in… · the same entry in another collection · chain A against A, TM-score 1.00
- P15291 · AlphaFold monomer V2.0 prediction for beta-1,4-galactosyltransferase 1 (P15291) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 P15291
- Elsewhere: RCSB PDB 2AGD · PDBe 2AGD · UniProt P15291
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