MolNFT v1 · #153624 · protein
Crystal structure of serratia marcescens chitinase B complexed with compound 2-8-14
6JK9: “Crystal structure of serratia marcescens chitinase B complexed with compound 2-8-14”. X-ray diffraction, 1 ligand (BU0), 4 pockets (best druggability 0.79). MolNFT v1 #153624 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6JK9
- Type
- protein
- Length
- 992 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitinase
- UniProt
- Q54276
- Ligands
- BU0
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Chitinase | protein | 496 | 33% helix, 20% strand | Q54276 |
Ligands and binding sites
- BU0 · 6-azanyl-2-oxidanylidene-N-[(1S)-1-phenylethyl]-7-(phenylmethyl)-1$L^{4},9-diaza-7-azoniatricyclo[8.4.0.0^{3,8}]tetradeca-1(14),3(8),4,6, 10,12-hexaene-5-carboxamide · ligand · 2 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.79 | 0.81 | 84 | BU0 |
| 2 | 1158 | 0.78 | 0.79 | 88 | BU0 |
| 3 | 164 | 0.51 | 0.79 | 33 | empty |
| 4 | 191 | 0.51 | 0.77 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 1495 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6JK9 · Crystal structure of Serratia marcescens Chitinase B complexed with compound 2-8-14 · 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 6JK9 · PDBe 6JK9 · UniProt Q54276
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.