Research workbench
Crystal structure of BRP39, a chitinase-like protein, at 2.6 angstorm resolution
Analyse Crystal structure of BRP39, a chitinase-like protein, at 2.6 angstorm resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XEP
- Type
- protein
- Length
- 2,158 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitinase-3-like protein 1
- UniProt
- Q61362
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chitinase-3-like protein 1 | protein | 362 | 36% helix, 22% strand | Q61362 |
| B, C | Chitinase-3-like protein 1 | protein | 360 | 37% helix, 22% strand | Q61362 |
| D | Chitinase-3-like protein 1 | protein | 361 | 37% helix, 22% strand | Q61362 |
| E | Chitinase-3-like protein 1 | protein | 358 | 36% helix, 22% strand | Q61362 |
| F | Chitinase-3-like protein 1 | protein | 357 | 36% helix, 22% strand | Q61362 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 606 | 0.80 | 0.85 | 71 | empty |
| 2 | 580 | 0.79 | 0.85 | 67 | empty |
| 3 | 554 | 0.79 | 0.85 | 67 | empty |
| 4 | 523 | 0.78 | 0.85 | 65 | empty |
| 5 | 542 | 0.77 | 0.84 | 65 | empty |
Interfaces
8 interfaces between chains.
- A–C · 838 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 808 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 806 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 785 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 744 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5XEP · Crystal structure of BRP39, a chitinase-like protein, at 2.6 Angstorm resolution · the same entry in another collection · chain F against F, TM-score 1.00
- Q61362 · AlphaFold monomer V2.0 prediction for chitinase-3-like protein 1 (Q61362) · a predicted model of the same protein · chain E 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 Q61362
- Elsewhere: RCSB PDB 5XEP · PDBe 5XEP · UniProt Q61362
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