Research workbench
Crystal structure of S. marcescens chitinase B in complex with the cyclic dipeptide inhibitor cyclo-(L-tyr-L-pro) at 1.85 a resolution
Analyse Crystal structure of S. marcescens chitinase B in complex with the cyclic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W1Y
- Type
- protein
- Length
- 993 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitinase B
- EC
- 3.2.1.14
- UniProt
- Q54276
- Ligands
- TYP, SO4
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chitinase B (EC 3.2.1.14) | protein | 496 | 32% helix, 21% strand | Q54276 |
| B | Chitinase B (EC 3.2.1.14) | protein | 497 | 32% helix, 20% strand | Q54276 |
Ligands and binding sites
- TYP · Cyclo-(L-tyrosine-L-proline) inhibitor · ligand · 7 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.81 | 0.82 | 85 | GOL, TYP |
| 2 | 1032 | 0.80 | 0.81 | 84 | GOL, TYP |
| 3 | 221 | 0.53 | 0.77 | 32 | empty |
| 4 | 176 | 0.50 | 0.77 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 1459 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1W1Y · Crystal structure of S. marcescens chitinase B in complex with the cyclic dipeptide… · 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 Q54276
- Elsewhere: RCSB PDB 1W1Y · PDBe 1W1Y · UniProt Q54276
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