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Crystal structure of the cysteine-rich domain of secreted frizzled- related protein 3 (sfrp-3;FZB)
Analyse Crystal structure of the cysteine-rich domain of secreted frizzled- related… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IJX
- Type
- protein
- Length
- 740 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Secreted frizzled-related sequence protein 3
- UniProt
- P97401
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F | Secreted frizzled-related sequence protein 3 | protein | 125 | 40% helix, 10% strand | P97401 |
| B | Secreted frizzled-related sequence protein 3 | protein | 120 | 40% helix, 11% strand | P97401 |
| D | Secreted frizzled-related sequence protein 3 | protein | 122 | 41% helix, 6% strand | P97401 |
| E | Secreted frizzled-related sequence protein 3 | protein | 123 | 41% helix, 11% strand | P97401 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 536 | 0.64 | 0.76 | 56 | empty |
| 2 | 335 | 0.56 | 0.75 | 28 | empty |
| 3 | 295 | 0.55 | 0.76 | 45 | empty |
| 4 | 103 | 0.40 | 0.76 | 14 | empty |
| 5 | 79 | 0.39 | 0.78 | 20 | empty |
Interfaces
8 interfaces between chains.
- A–C · 1209 Ų buried · 18 hydrogen bonds · protein-protein
- B–E · 1179 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 495 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 333 Ų buried · 0 hydrogen bonds · protein-protein
- D–E · 302 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide (disulfide).
Compared structures
- 1IJX · Crystal structure of the cysteine-rich domain of secreted frizzled-related protein 3… · the same entry in another collection · chain F against F, TM-score 1.00
- P97401 · AlphaFold monomer V2.0 prediction for secreted frizzled-related protein 3 (P97401) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 P97401
- Elsewhere: RCSB PDB 1IJX · PDBe 1IJX · UniProt P97401
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