Research workbench
Crystal structure of exohep from bacteroides intestinalis dsm 17393 complexed with disaccharide product
Analyse Crystal structure of exohep from bacteroides intestinalis dsm 17393 complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LJA
- Type
- protein
- Length
- 841 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heparinase II/III-like protein
- UniProt
- B3C5J6
- Ligands
- UAP, SGN, CA
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 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
- UAP · 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid · ligand · chains A
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · 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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