MolNFT v1 · #8427 · protein
Complex of a chitinase with the natural product cyclopentapeptide argifin from gliocladium
1H0I · Chitinase B: “Complex of a chitinase with the natural product cyclopentapeptide argifin from gliocladium”. X-ray diffraction, 3 ligands (IAS, DAL, SO4), 6 pockets (best druggability 0.76). MolNFT v1 #8427 on GenesisL1: 3D structure…
- PDB
- 1H0I
- Type
- protein
- Length
- 999 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitinase B; Argifin
- EC
- 3.2.1.14
- UniProt
- P11797
- Ligands
- IAS, DAL, SO4
- Pockets
- 6 · 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 | 33% helix, 20% strand | P11797 |
| C, D | Argifin | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- IAS · Beta-L-aspartic acid · ligand · 2 copies · chains A, C, B, D
- DAL · D-alanine · ligand · 2 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 368 | 0.76 | 0.86 | 41 | SO4 |
| 2 | 376 | 0.75 | 0.85 | 41 | empty |
| 3 | 620 | 0.73 | 0.80 | 56 | IAS, DAL, GOL, SO4 |
| 4 | 619 | 0.73 | 0.80 | 50 | IAS, DAL, SO4 |
| 5 | 236 | 0.54 | 0.77 | 41 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1355 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 467 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 455 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified, 4 covalent, 2 disulfide (nonstandard, covalent ligand, disulfide).
Compared structures
- 1H0I · Complex of a chitinase with the natural product cyclopentapeptide argifin from Gliocladium · the same entry in another collection · chain B against B, 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 0.99
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 1H0I · PDBe 1H0I · UniProt P11797
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