Research workbench
Crystal structure of galnac-T4 in complex with the monoglycopeptide 3
Analyse Crystal structure of galnac-T4 in complex with the monoglycopeptide 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NQA
- Type
- protein
- Length
- 1,029 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polypeptide N-acetylgalactosaminyltransferase 4; Monoglycopeptide 3
- EC
- 2.4.1.41
- UniProt
- Q8N4A0
- Ligands
- NGA
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polypeptide N-acetylgalactosaminyltransferase 4 (EC 2.4.1.41) | protein | 514 | 28% helix, 23% strand | Q8N4A0 |
| B | Polypeptide N-acetylgalactosaminyltransferase 4 (EC 2.4.1.41) | protein | 514 | 28% helix, 23% strand | Q8N4A0 |
| G | Monoglycopeptide 3 | protein | 1 | 0% helix, 0% strand | — |
Ligands and binding sites
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 2 copies · chains A, B, G
- EDO · 1,2-ethanediol · additive · 71 copies · chains A, B
- GOL · Glycerol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 840 | 0.70 | 0.76 | 91 | EDO, GOL |
| 2 | 575 | 0.67 | 0.77 | 60 | EDO |
| 3 | 432 | 0.60 | 0.75 | 53 | EDO |
| 4 | 266 | 0.57 | 0.77 | 37 | EDO |
| 5 | 324 | 0.57 | 0.76 | 35 | empty |
Interfaces
2 interfaces between chains.
- A–B · 359 Ų buried · 6 hydrogen bonds · protein-protein
- B–G · 44 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 glycan (disulfide, O-glycosylation).
Compared structures
- 5NQA · Crystal structure of GalNAc-T4 in complex with the monoglycopeptide 3 · the same entry in another collection · chain A against A, TM-score 1.00
- Q8N4A0 · AlphaFold monomer V2.0 prediction for polypeptide N-acetylgalactosaminyltransferase 4… · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q8N4A0
- Elsewhere: RCSB PDB 5NQA · PDBe 5NQA · UniProt Q8N4A0
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