Research workbench
Complex of a chitinase with the natural product cyclopentapeptide argadin from clonostachys
Analyse Complex of a chitinase with the natural product cyclopentapeptide argadin from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1H0G
- Type
- protein
- Length
- 999 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitinase B; Argadin
- EC
- 3.2.1.14
- UniProt
- P11797
- Ligands
- HSE, UN1
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chitinase B (EC 3.2.1.14) | protein | 496 | 32% helix, 21% strand | P11797 |
| B | Chitinase B (EC 3.2.1.14) | protein | 497 | 32% helix, 20% strand | P11797 |
| C, D | Argadin | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- HSE · L-homoserine · ligand · 2 copies · chains B, C, A, D
- UN1 · 2-aminohexanedioic acid · ligand · 2 copies · chains B, C, A, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.76 | 0.96 | 21 | UN1 |
| 2 | 268 | 0.76 | 0.88 | 37 | UN1 |
| 3 | 531 | 0.70 | 0.79 | 50 | HSE |
| 4 | 531 | 0.70 | 0.79 | 48 | GOL |
| 5 | 225 | 0.53 | 0.77 | 38 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1402 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 492 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 488 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 73 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 72 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent, 2 d-amino, 2 disulfide, 2 modified (covalent ligand, D-amino acid, disulfide, nonstandard).
Compared structures
- 1H0G · Complex of a chitinase with the natural product cyclopentapeptide argadin from… · the same entry in another collection · chain A against A, TM-score 1.00
- P11797 · AlphaFold monomer V2.0 prediction for chitinase B (P11797) · a predicted model of the same protein · chain B 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 P11797
- Elsewhere: RCSB PDB 1H0G · PDBe 1H0G · UniProt P11797
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