Research workbench
Chitinase B from serratia marcescens wildtype in complex with catalytic intermediate
Analyse Chitinase B from serratia marcescens wildtype in complex with catalytic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1E6Z
- 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
- NGO, NAG, SO4
- Pockets
- 4 · best druggability 0.79
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, 20% strand | Q54276 |
| B | Chitinase B (EC 3.2.1.14) | protein | 498 | 32% helix, 20% strand | Q54276 |
Ligands and binding sites
- NGO · 2-methyl-4,5-dihydro-(1,2-dideoxy-alpha-D-glucopyranoso)[2,1-D]-1,3-oxazole · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 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 | 1116 | 0.79 | 0.80 | 90 | NAG, NGO |
| 2 | 1106 | 0.77 | 0.79 | 88 | NGO, NAG |
| 3 | 215 | 0.53 | 0.78 | 37 | empty |
| 4 | 126 | 0.45 | 0.78 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1383 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1E6Z · Chitinase B from serratia marcescens wildtype in complex with catalytic intermediate · 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 1E6Z · PDBe 1E6Z · UniProt Q54276
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