Research workbench
Serratia marcescens chitinase B complexed with azide inhibitor
Analyse Serratia marcescens chitinase B complexed with azide inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WD2
- Type
- protein
- Length
- 497 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitinase B
- EC
- 3.2.1.14
- UniProt
- P11797
- Ligands
- A1L, SO4
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chitinase B (EC 3.2.1.14) | protein | 497 | 31% helix, 20% strand | P11797 |
Ligands and binding sites
- A1L · [2-[[(2S)-1-[bis(phenylmethyl)amino]-5-[[N-(methylcarbamoyl)carbamimidoyl]amino]-1-oxidanylidene-pentan-2-yl]amino]-2-oxidanylidene-ethyl]-diazonio-azanide · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 9 copies · chains A
- DTD · Dithiane diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 819 | 0.74 | 0.78 | 66 | A1L |
| 2 | 61 | 0.37 | 0.79 | 13 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
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 P11797
- Elsewhere: RCSB PDB 3WD2 · PDBe 3WD2 · UniProt P11797
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