MolNFT v2 · #156840 · protein
Crystal Structure of exoHep from Bacteroides intestinalis DSM 17393 complexed with disaccharide product
6LJA · Heparinase II/III-like protein: “Crystal Structure of exoHep from Bacteroides intestinalis DSM 17393 complexed with disaccharide product”. X-ray diffraction at 1.978, 3 ligands (SGN, UAP, CA), 8 pockets (best druggability 0.78).…
- PDB
- 6LJA
- Type
- protein
- Length
- 841 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.978
- Source
- Bacteroides intestinalis DSM 17393
- Molecule
- Heparinase II/III-like protein
- UniProt
- B3C5J6
- Ligands
- SGN, UAP, CA
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · resolution 1.978 · 1 distinct chain · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heparinase II/III-like protein | protein | 841 | 33% helix, 23% strand | B3C5J6 |
Ligands and binding sites
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · chains A
- UAP · 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid · sugar · chains A
- CA · Calcium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 884 | 0.78 | 0.81 | 86 | SGN, UAP |
| 2 | 440 | 0.75 | 0.84 | 50 | empty |
| 3 | 760 | 0.75 | 0.79 | 48 | empty |
| 4 | 90 | 0.44 | 0.79 | 19 | empty |
| 5 | 62 | 0.40 | 0.80 | 18 | empty |
Compared structures
- 6LJA · Crystal structure of exohep from bacteroides intestinalis dsm 17393 complexed with… · 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 B3C5J6
- Elsewhere: RCSB PDB 6LJA · PDBe 6LJA · UniProt B3C5J6
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