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Crystal structure of mutant (D318N) bacillus subtilis family 3 glycoside hydrolase (nagz) in complex with glcnac-murnac (space group P1)
Analyse Crystal structure of mutant (D318N) bacillus subtilis family 3 glycoside… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GYJ
- Type
- protein
- Length
- 1,235 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized lipoprotein ybbd
- UniProt
- P40406
- Ligands
- MUB, NAG
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized lipoprotein ybbd | protein | 618 | 42% helix, 15% strand | P40406 |
| B | Uncharacterized lipoprotein ybbd | protein | 617 | 42% helix, 15% strand | P40406 |
Ligands and binding sites
- MUB · N-acetyl-alpha-muramic acid · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.81 | 0.83 | 84 | MUB, NAG |
| 2 | 1085 | 0.81 | 0.83 | 106 | MUB, NAG |
| 3 | 209 | 0.64 | 0.84 | 30 | empty |
| 4 | 219 | 0.61 | 0.82 | 30 | empty |
| 5 | 205 | 0.54 | 0.78 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 953 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4GYJ · Crystal structure of mutant (D318N) bacillus subtilis family 3 glycoside hydrolase (nagz)… · the same entry in another collection · chain A against A, TM-score 1.00
- P40406 · AlphaFold monomer V2.0 prediction for beta-hexosaminidase (P40406) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P40406
- Elsewhere: RCSB PDB 4GYJ · PDBe 4GYJ · UniProt P40406
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