MolNFT v1 · #125400 · protein
Crystal structure of BVGH123 with bond transition state analog galthiazoline.
5L7V · Glycoside hydrolase: “Crystal structure of BVGH123 with bond transition state analog galthiazoline.”. X-ray diffraction, 1 ligand (GNL), 11 pockets (best druggability 0.79). MolNFT v1 #125400 on GenesisL1: 3D structure, binding…
- PDB
- 5L7V
- Type
- protein
- Length
- 1,125 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase
- UniProt
- A6L2E5
- Ligands
- GNL
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoside hydrolase | protein | 563 | 29% helix, 29% strand | A6L2E5 |
| B | Glycoside hydrolase | protein | 562 | 29% helix, 29% strand | A6L2E5 |
Ligands and binding sites
- GNL · (3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methyl-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 922 | 0.79 | 0.81 | 86 | GNL |
| 2 | 140 | 0.54 | 0.81 | 30 | empty |
| 3 | 149 | 0.54 | 0.81 | 22 | empty |
| 4 | 162 | 0.53 | 0.80 | 21 | empty |
| 5 | 75 | 0.52 | 0.85 | 17 | GNL |
Interfaces
1 interface between chains.
- A–B · 364 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5L7V · Crystal Structure of BvGH123 with bond transition state analog Galthiazoline. · 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 5L7V · PDBe 5L7V · UniProt A6L2E5
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