Research workbench
Crystal structure of burkholderia pseudomallei heparanase in complex with covalent inhibitor GR109
Analyse Crystal structure of burkholderia pseudomallei heparanase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PRB
- Type
- protein
- Length
- 875 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GLYCO_HYDRO_44 domain-containing protein
- UniProt
- Q63T97
- Ligands
- 8I4, NGY
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GLYCO_HYDRO_44 domain-containing protein | protein | 437 | 30% helix, 31% strand | Q63T97 |
| B | GLYCO_HYDRO_44 domain-containing protein | protein | 438 | 30% helix, 31% strand | Q63T97 |
Ligands and binding sites
- 8I4 · (2R,3S,5R,6R)-2,3,4,5,6-pentakis(oxidanyl)cyclohexane-1-carboxylic acid · ligand · 2 copies · chains A, B
- NGY · 2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 613 | 0.75 | 0.81 | 65 | EDO |
| 2 | 577 | 0.74 | 0.81 | 61 | EDO |
| 3 | 214 | 0.53 | 0.77 | 33 | empty |
| 4 | 195 | 0.52 | 0.78 | 30 | empty |
| 5 | 176 | 0.47 | 0.76 | 35 | 8I4, NGY |
Interfaces
1 interface between chains.
- A–B · 1175 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 7PRB · Crystal structure of Burkholderia pseudomallei heparanase in complex with covalent… · the same entry in another collection · 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 Q63T97
- Elsewhere: RCSB PDB 7PRB · PDBe 7PRB · UniProt Q63T97
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