MolNFT v1 · #88639 · protein
Galnac-T2 crystal soaked with udp-5SGALNAC, MEA2 peptide and manganese (lower resolution dataset)
4D11 · Polypeptide galnac-transferase T2: “Galnac-T2 crystal soaked with udp-5SGALNAC, MEA2 peptide and manganese (lower resolution dataset)”. X-ray diffraction, 3 ligands (UDP, BBK, MN), 20 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 4D11
- Type
- protein
- Length
- 2,684 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polypeptide galnac-transferase T2; Peptide
- UniProt
- Q10471
- Ligands
- UDP, BBK, MN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polypeptide galnac-transferase T2 | protein | 491 | 29% helix, 25% strand | Q10471 |
| B | Polypeptide galnac-transferase T2 | protein | 482 | 29% helix, 26% strand | Q10471 |
| C | Polypeptide galnac-transferase T2 | protein | 436 | 30% helix, 25% strand | Q10471 |
| D, E | Polypeptide galnac-transferase T2 | protein | 487 | 29% helix, 26% strand | Q10471 |
| F | Polypeptide galnac-transferase T2 | protein | 276 | 29% helix, 25% strand | Q10471 |
| L, O, P, X, Z | Peptide | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 6 copies · chains A, Z, B, P, C, L, D, X, E, O, F
- BBK · 2-acetamido-2-deoxy-5-thio-alpha-D-galactopyranose · ligand · 4 copies · chains A, B, D, E
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1011 | 0.84 | 0.85 | 128 | BBK |
| 2 | 255 | 0.81 | 0.93 | 45 | UDP |
| 3 | 264 | 0.80 | 0.92 | 44 | MN, UDP |
| 4 | 376 | 0.79 | 0.89 | 44 | MN, UDP |
| 5 | 532 | 0.79 | 0.85 | 50 | MN, UDP |
Interfaces
14 interfaces between chains.
- D–E · 1726 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1520 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 636 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 522 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 441 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 disulfide (disulfide).
Compared structures
- 4D11 · GalNAc-T2 crystal soaked with UDP-5SGalNAc, mEA2 peptide and manganese (Lower resolution… · 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 F against A, TM-score 0.99
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 4D11 · PDBe 4D11 · UniProt Q10471
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.