MolNFT v1 · #119410 · protein
Crystal structure of galnac-T2 in complex with compound 16D
5FV9: “Crystal structure of galnac-T2 in complex with compound 16D”. X-ray diffraction, 3 ligands (UDP, Y6W, MN), 20 pockets (best druggability 0.82). MolNFT v1 #119410 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5FV9
- Type
- protein
- Length
- 2,856 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galnac-T2
- UniProt
- Q10471
- Ligands
- UDP, Y6W, MN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Galnac-T2 | protein | 483 | 29% helix, 26% strand | Q10471 |
| B | Galnac-T2 | protein | 484 | 28% helix, 26% strand | Q10471 |
| C | Galnac-T2 | protein | 482 | 28% helix, 26% strand | Q10471 |
| D | Galnac-T2 | protein | 443 | 31% helix, 20% strand | Q10471 |
| F | Galnac-T2 | protein | 481 | 28% helix, 27% strand | Q10471 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- Y6W · [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl hydrogen (S)-{3-[(2R,3R,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]propyl}phosphonate · ligand · 3 copies · chains B, E, F
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B, C, E, F
- GOL · Glycerol · additive · 5 copies · chains A, C, 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.82 | 0.83 | 125 | empty |
| 2 | 514 | 0.76 | 0.84 | 66 | empty |
| 3 | 725 | 0.71 | 0.77 | 75 | UDP |
| 4 | 717 | 0.70 | 0.77 | 67 | UDP |
| 5 | 623 | 0.70 | 0.78 | 60 | EDO |
Interfaces
7 interfaces between chains.
- C–D · 1672 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1458 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 445 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 442 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 347 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 29 disulfide (disulfide).
Compared structures
- 5FV9 · Crystal structure of GalNAc-T2 in complex with compound 16d · the same entry in another collection · chain F against F, 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 5FV9 · PDBe 5FV9 · UniProt Q10471
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