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Crystal structure of exohep-Y390A/H555A complexed with a tetrasaccharide substrate
Analyse Crystal structure of exohep-Y390A/H555A complexed with a tetrasaccharide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LJL
- 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
- GCD, SGN, IDS, CA
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heparinase II/III-like protein | protein | 841 | 31% helix, 23% strand | B3C5J6 |
Ligands and binding sites
- GCD · 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid · ligand · chains A
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · 2 copies · chains A
- IDS · 2-O-sulfo-alpha-L-idopyranuronic 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 | 1071 | 0.80 | 0.82 | 111 | SGN, IDS, GCD |
| 2 | 501 | 0.75 | 0.83 | 61 | empty |
| 3 | 662 | 0.74 | 0.80 | 51 | empty |
| 4 | 112 | 0.41 | 0.77 | 21 | empty |
| 5 | 53 | 0.31 | 0.76 | 13 | empty |
Compared structures
- 6LJL · Crystal Structure of exoHep-Y390A/H555A complexed with a tetrasaccharide substrate · 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 6LJL · PDBe 6LJL · UniProt B3C5J6
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