MolNFT v1 · #125399 · protein
Crystal structure of BVGH123 with bound galnac
5L7U · Glycoside hydrolase: “Crystal structure of BVGH123 with bound galnac”. X-ray diffraction, 2 ligands (NGA, CL), 14 pockets (best druggability 0.53). MolNFT v1 #125399 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5L7U
- Type
- protein
- Length
- 1,115 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase
- UniProt
- A6L2E5
- Ligands
- NGA, CL
- Pockets
- 14 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoside hydrolase | protein | 554 | 29% helix, 29% strand | A6L2E5 |
| B | Glycoside hydrolase | protein | 561 | 29% helix, 29% strand | A6L2E5 |
Ligands and binding sites
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 180 | 0.53 | 0.79 | 22 | empty |
| 2 | 128 | 0.53 | 0.81 | 20 | NGA |
| 3 | 178 | 0.53 | 0.79 | 46 | empty |
| 4 | 180 | 0.51 | 0.78 | 24 | empty |
| 5 | 127 | 0.50 | 0.80 | 23 | NGA |
Interfaces
1 interface between chains.
- A–B · 1120 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5L7U · Crystal structure of BvGH123 with bound GalNAc · 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 A6L2E5
- Elsewhere: RCSB PDB 5L7U · PDBe 5L7U · UniProt A6L2E5
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