Research workbench
Crystal structure of signaling protein spb-40 complexed with 5- hydroxymethyl oxalanetriol at 2.80 a resolution
Analyse Crystal structure of signaling protein spb-40 complexed with 5- hydroxymethyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MAV
- Type
- protein
- Length
- 361 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitinase-3-like protein 1
- UniProt
- Q7YS85
- Ligands
- RIB, NAG
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chitinase-3-like protein 1 | protein | 361 | 36% helix, 23% strand | Q7YS85 |
Ligands and binding sites
- RIB · alpha-D-ribofuranose · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 405 | 0.65 | 0.78 | 40 | RIB |
| 2 | 155 | 0.59 | 0.83 | 21 | empty |
| 3 | 61 | 0.36 | 0.78 | 13 | empty |
Modifications
Observed in the structure: 2 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4MAV · Crystal structure of signaling protein SPB-40 complexed with 5-hydroxymethyl oxalanetriol… · the same entry in another collection · chain A against A, TM-score 1.00
- Q7YS85 · AlphaFold monomer V2.0 prediction for chitinase-3-like protein 1 (Q7YS85) · a predicted model of the same protein · chain A 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 Q7YS85
- Elsewhere: RCSB PDB 4MAV · PDBe 4MAV · UniProt Q7YS85
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