MolNFT v1 · #152891 · protein
Crystal structure of galnac-T7 with udp, galnac and MN2+
6IWR · N-acetylgalactosaminyltransferase 7: “Crystal structure of galnac-T7 with udp, galnac and MN2+”. X-ray diffraction, 4 ligands (UDP, UD2, NAG), 20 pockets (best druggability 0.75). MolNFT v1 #152891 on GenesisL1: 3D structure…
- PDB
- 6IWR
- Type
- protein
- Length
- 3,268 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylgalactosaminyltransferase 7
- EC
- 2.4.1.-
- UniProt
- Q86SF2
- Ligands
- UDP, UD2, NAG, MN
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F | N-acetylgalactosaminyltransferase 7 (EC 2.4.1.-) | protein | 546 | 27% helix, 25% strand | Q86SF2 |
| D | N-acetylgalactosaminyltransferase 7 (EC 2.4.1.-) | protein | 538 | 27% helix, 25% strand | Q86SF2 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains D
- UD2 · Uridine-diphosphate-N-acetylgalactosamine · ligand · chains C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains D
- 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 946 | 0.75 | 0.78 | 92 | empty |
| 2 | 779 | 0.72 | 0.78 | 70 | empty |
| 3 | 599 | 0.72 | 0.79 | 71 | MN |
| 4 | 644 | 0.71 | 0.78 | 77 | MN |
| 5 | 506 | 0.70 | 0.80 | 60 | MN |
Interfaces
9 interfaces between chains.
- A–B · 958 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 795 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 618 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 540 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 399 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide (disulfide).
Compared structures
- 6IWR · Crystal structure of GalNAc-T7 with UDP, GalNAc and Mn2+ · the same entry in another collection · chain F against F, TM-score 1.00
- Q86SF2 · AlphaFold monomer V2.0 prediction for N-acetylgalactosaminyltransferase 7 (Q86SF2) · a predicted model of the same protein · chain D against A, TM-score 1.00
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 Q86SF2
- Elsewhere: RCSB PDB 6IWR · PDBe 6IWR · UniProt Q86SF2
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