Research workbench
Structure of BT4656 in complex with its substrate D-glucosamine-2-N, 6-O-disulfate.
Analyse Structure of BT4656 in complex with its substrate D-glucosamine-2-N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5G2V
- Type
- protein
- Length
- 494 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylglucosamine-6-sulfatase
- EC
- 3.1.6.14
- UniProt
- Q89YS5
- Ligands
- SGN, CA, NO3
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetylglucosamine-6-sulfatase (EC 3.1.6.14) | protein | 494 | 34% helix, 17% strand | Q89YS5 |
Ligands and binding sites
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · chains A
- CA · Calcium ion · metal · chains A
- NO3 · Nitrate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.47 | 0.75 | 29 | empty |
| 2 | 138 | 0.46 | 0.78 | 28 | SGN |
Compared structures
- 5G2V · Structure of BT4656 in complex with its substrate D-Glucosamine-2-N, 6-O-disulfate. · the same entry in another collection · chain A against A, TM-score 1.00
- Q89YS5 · AlphaFold monomer V2.0 prediction for N-acetylglucosamine-6-O-sulfatase (Q89YS5) · a predicted model of the same protein · chain A 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 Q89YS5
- Elsewhere: RCSB PDB 5G2V · PDBe 5G2V · UniProt Q89YS5
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