Research workbench
Crystal structure of serratia marcescens chitinase B complexed with compound 2-8-S2
Analyse Crystal structure of serratia marcescens chitinase B complexed with compound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JKF
- Type
- protein
- Length
- 993 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitinase
- UniProt
- Q54276
- Ligands
- BV0
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chitinase | protein | 496 | 32% helix, 20% strand | Q54276 |
| B | Chitinase | protein | 497 | 33% helix, 21% strand | Q54276 |
Ligands and binding sites
- BV0 · 6-azanyl-11-methyl-2-oxidanylidene-7-[[(2R)-oxolan-2-yl]methyl]-N-(pyridin-3-ylmethyl)-1,9-diaza-7-azoniatricyclo[8.4.0.0^{3,8}]tetradeca-3(8),4,6,9,11, 13-hexaene-5-carboxamide · ligand · 3 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 988 | 0.80 | 0.81 | 86 | BV0 |
| 2 | 976 | 0.75 | 0.78 | 77 | BV0 |
| 3 | 169 | 0.50 | 0.77 | 34 | empty |
| 4 | 165 | 0.48 | 0.77 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1465 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6JKF · Crystal structure of Serratia marcescens Chitinase B complexed with compound 2-8-s2 · 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 6JKF · PDBe 6JKF · UniProt Q54276
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