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Crystal structure of S. marcescens chitinase B in complex with the cyclic dipeptide inhibitor cyclo-(gly-L-pro) at 2.1 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
- 1W1P
- Type
- protein
- Length
- 995 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
- GIO, SO4
- Pockets
- 3 · best druggability 0.80
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 | 497 | 32% helix, 21% strand | Q54276 |
| B | Chitinase B (EC 3.2.1.14) | protein | 498 | 32% helix, 20% strand | Q54276 |
Ligands and binding sites
- GIO · Cyclo-(glycine-L-proline) inhibitor · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- GOL · Glycerol · additive · 20 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.80 | 0.81 | 113 | GOL, GIO |
| 2 | 1132 | 0.79 | 0.80 | 89 | GOL, GIO |
| 3 | 167 | 0.49 | 0.78 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1405 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1W1P · Crystal structure of S. marcescens chitinase B in complex with the cyclic dipeptide… · the same entry in another collection · chain B against B, 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 1W1P · PDBe 1W1P · UniProt Q54276
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