Research workbench
Crystal structure of the human GalNAc-T4 in complex with UDP, manganese and the diglycopeptide 6.
Analyse Crystal structure of the human GalNAc-T4 in complex with UDP, manganese and the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H0B
- Type
- protein
- Length
- 1,051 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Polypeptide N-acetylgalactosaminyltransferase 4…
- EC
- 2.4.1.41
- UniProt
- Q8N4A0
- Ligands
- UDP, NGA, MN
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · resolution 1.8 · 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 | 515 | 29% helix, 23% strand | Q8N4A0 |
| B | Polypeptide N-acetylgalactosaminyltransferase 4 (EC 2.4.1.41) | protein | 521 | 28% helix, 23% strand | Q8N4A0 |
| F | Ala-thr-gly-ala-gly-ala-gly-ala-gly-thr-thr-pro-gly-pro-gly | protein | 15 | 0% helix, 7% strand | — |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains B, F
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 2 copies · chains B, F
- MN · Manganese (II) ion · metal · chains B
- EDO · 1,2-ethanediol · additive · 36 copies · chains A, B, F
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.80 | 0.93 | 42 | MN, UDP, EDO |
| 2 | 465 | 0.64 | 0.77 | 52 | empty |
| 3 | 525 | 0.63 | 0.76 | 68 | EDO |
| 4 | 448 | 0.61 | 0.75 | 51 | EDO |
| 5 | 269 | 0.54 | 0.76 | 28 | EDO |
Interfaces
2 interfaces between chains.
- B–F · 573 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 397 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan (disulfide, O-glycosylation).
Compared structures
- 6H0B · Crystal structure of the human galnac-T4 in complex with udp, manganese and the… · 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 B against A, TM-score 0.98
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 6H0B · PDBe 6H0B · UniProt Q8N4A0
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