MolNFT v1 · #100996 · protein
Structure of maltose binding protein fusion to 2-O-sulfotransferase with bound heptasaccharide and pap
4NDZ · Maltose-binding periplasmic protein, heparan sulfate 2-O…: “Structure of maltose binding protein fusion to 2-O-sulfotransferase with bound heptasaccharide and pap”. X-ray diffraction, 7 ligands (GNS, A3P, IDR), 20 pockets (best…
- PDB
- 4NDZ
- Type
- protein
- Length
- 3,558 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic protein, heparan sulfate 2-O- sulfotransferase 1 fusion
- EC
- 2.8.2.-
- UniProt
- P0AEX9, Q76KB1
- Ligands
- GNS, A3P, IDR, NPO, BDP, GLC, NDG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltose-binding periplasmic protein, heparan sulfate 2-O- sulfotransferase 1 fusion (EC 2.8.2.-) | protein | 287 | 47% helix, 15% strand | P0AEX9, Q76KB1 |
| B, D, E, F | Maltose-binding periplasmic protein, heparan sulfate 2-O- sulfotransferase 1 fusion (EC 2.8.2.-) | protein | 654 | 44% helix, 16% strand | P0AEX9, Q76KB1 |
| C | Maltose-binding periplasmic protein, heparan sulfate 2-O- sulfotransferase 1 fusion (EC 2.8.2.-) | protein | 655 | 45% helix, 16% strand | P0AEX9, Q76KB1 |
Ligands and binding sites
- GNS · 2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose · ligand · 10 copies · chains A, B, C, D, E, F
- A3P · Adenosine-3'-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- IDR · alpha-L-idopyranuronic acid · ligand · 5 copies · chains A, B, D, E, F
- NPO · P-nitrophenol · ligand · 4 copies · chains A, B, D, E
- BDP · beta-D-glucopyranuronic acid · sugar · 15 copies · chains A, B, C, D, E, F
- GLC · alpha-D-glucopyranose · sugar · 10 copies · chains B, C, D, E, F
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 5 copies · chains B, C, E, F, D
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 | 596 | 0.89 | 0.95 | 112 | empty |
| 2 | 462 | 0.88 | 0.96 | 87 | empty |
| 3 | 878 | 0.83 | 0.85 | 113 | empty |
| 4 | 488 | 0.80 | 0.87 | 87 | empty |
| 5 | 424 | 0.78 | 0.87 | 37 | empty |
Interfaces
9 interfaces between chains.
- D–E · 2292 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 2210 Ų buried · 33 hydrogen bonds · protein-protein
- D–F · 2071 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1984 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1846 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 4NDZ · Structure of Maltose Binding Protein fusion to 2-O-Sulfotransferase with bound… · the same entry in another collection · chain F against F, TM-score 1.00
- Q76KB1 · AlphaFold monomer V2.0 prediction for heparan sulfate 2-O-sulfotransferase 1 (Q76KB1) · a predicted model of the same protein · chain A 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 P0AEX9
- Every structure of UniProt Q76KB1
- Elsewhere: RCSB PDB 4NDZ · PDBe 4NDZ · UniProt P0AEX9 · UniProt Q76KB1
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