Research workbench
Structure of GH84 with ligand
Analyse Structure of GH84 with ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ABE
- Type
- protein
- Length
- 1,351 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-glcnacase BT_4395
- UniProt
- Q89ZI2
- Ligands
- XQO, CA
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-glcnacase BT_4395 | protein | 681 | 39% helix, 20% strand | Q89ZI2 |
| B | O-glcnacase BT_4395 | protein | 670 | 40% helix, 20% strand | Q89ZI2 |
Ligands and binding sites
- XQO · 2-[(2S,3S,4R,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)-1-pentyl-pyrrolidin-2-yl]-N-methyl-ethanamide · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 480 | 0.67 | 0.78 | 50 | empty |
| 2 | 422 | 0.64 | 0.78 | 47 | empty |
| 3 | 310 | 0.60 | 0.78 | 35 | empty |
| 4 | 86 | 0.54 | 0.85 | 19 | XQO |
| 5 | 92 | 0.54 | 0.84 | 19 | XQO |
Interfaces
1 interface between chains.
- A–B · 1094 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- Q89ZI2 · AlphaFold monomer V2.0 prediction for O-glcnacase BT_4395 (Q89ZI2) · 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 Q89ZI2
- Elsewhere: RCSB PDB 5ABE · PDBe 5ABE · UniProt Q89ZI2
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