MolNFT v1 · #60088 · protein
Crystal structure of aspergillus fumigatus chitinase B1 in complex with tetrapeptide
3CHF: “Crystal structure of aspergillus fumigatus chitinase B1 in complex with tetrapeptide”. X-ray diffraction, 2 ligands (ACE, SO4), 8 pockets (best druggability 0.64). MolNFT v1 #60088 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3CHF
- Type
- protein
- Length
- 797 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitinase; Argifin
- EC
- 3.2.1.14
- UniProt
- Q873X9
- Ligands
- ACE, SO4
- Pockets
- 8 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chitinase (EC 3.2.1.14) | protein | 395 | 38% helix, 20% strand | Q873X9 |
| B | Chitinase (EC 3.2.1.14) | protein | 394 | 38% helix, 20% strand | Q873X9 |
| C, D | Argifin | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 14 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 166 | 0.64 | 0.85 | 28 | empty |
| 2 | 156 | 0.63 | 0.86 | 27 | empty |
| 3 | 76 | 0.52 | 0.85 | 14 | empty |
| 4 | 154 | 0.47 | 0.77 | 22 | empty |
| 5 | 82 | 0.47 | 0.81 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–D · 451 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 446 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 394 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 2 covalent, 2 d-amino (nonstandard, covalent ligand, D-amino acid).
Compared structures
- 3CHF · Crystal structure of Aspergillus fumigatus chitinase B1 in complex with tetrapeptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q873X9 · AlphaFold monomer V2.0 prediction for endochitinase B1 (Q873X9) · 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 Q873X9
- Elsewhere: RCSB PDB 3CHF · PDBe 3CHF · UniProt Q873X9
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