MolNFT v1 · #88631 · protein
Galnac-T2 crystal soaked with udp-galnac, EA2 peptide and manganese
4D0T · Polypeptide N-acetylgalactosaminyltransferase 2: “Galnac-T2 crystal soaked with udp-galnac, EA2 peptide and manganese”. X-ray diffraction, 4 ligands (UD2, UDP, NGA), 20 pockets (best druggability 0.83). MolNFT v1 #88631 on…
- PDB
- 4D0T
- Type
- protein
- Length
- 2,976 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polypeptide N-acetylgalactosaminyltransferase 2; Peptide
- EC
- 2.4.1.41
- UniProt
- Q10471
- Ligands
- UD2, UDP, NGA, MN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polypeptide N-acetylgalactosaminyltransferase 2 (EC 2.4.1.41) | protein | 496 | 29% helix, 24% strand | Q10471 |
| B, C, D, E | Polypeptide N-acetylgalactosaminyltransferase 2 (EC 2.4.1.41) | protein | 495 | 29% helix, 24% strand | Q10471 |
| F | Polypeptide N-acetylgalactosaminyltransferase 2 (EC 2.4.1.41) | protein | 487 | 29% helix, 24% strand | Q10471 |
| P | Peptide | protein | 7 | 0% helix, 0% strand | — |
| Z | Peptide | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- UD2 · Uridine-diphosphate-N-acetylgalactosamine · ligand · 5 copies · chains A, B, Z, D, E, F
- UDP · Uridine-5'-diphosphate · ligand · chains C, P
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · chains C, P
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, C, P, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.83 | 0.96 | 48 | MN, UDP, EDO, NGA |
| 2 | 897 | 0.82 | 0.84 | 87 | empty |
| 3 | 265 | 0.82 | 0.93 | 46 | MN, UD2 |
| 4 | 1033 | 0.81 | 0.82 | 125 | UD2 |
| 5 | 816 | 0.81 | 0.84 | 91 | empty |
Interfaces
12 interfaces between chains.
- C–F · 1728 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1622 Ų buried · 16 hydrogen bonds · protein-protein
- B–E · 1466 Ų buried · 10 hydrogen bonds · protein-protein
- C–P · 536 Ų buried · 6 hydrogen bonds · protein-protein
- B–Z · 501 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide, 1 glycan (disulfide, O-glycosylation).
Compared structures
- 4D0T · GalNAc-T2 crystal soaked with UDP-GalNAc, EA2 peptide and manganese · the same entry in another collection · chain Z against Z, TM-score 1.00
- Q10471 · AlphaFold monomer V2.0 prediction for polypeptide N-acetylgalactosaminyltransferase 2… · 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 Q10471
- Elsewhere: RCSB PDB 4D0T · PDBe 4D0T · UniProt Q10471
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