Research workbench
Wild type single insulin-like growth factor binding domain protein (sibd-1) from cupiennius salei
Analyse Wild type single insulin-like growth factor binding domain protein (sibd-1)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZXB
- Type
- protein
- Length
- 267 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single insulin-like growth factor-binding domain protein-1
- UniProt
- G4V4F9
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Single insulin-like growth factor-binding domain protein-1 | protein | 66 | 9% helix, 29% strand | G4V4F9 |
| B | Single insulin-like growth factor-binding domain protein-1 | protein | 67 | 4% helix, 28% strand | G4V4F9 |
| C | Single insulin-like growth factor-binding domain protein-1 | protein | 68 | 9% helix, 28% strand | G4V4F9 |
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 | 624 | 0.81 | 0.86 | 55 | empty |
| 2 | 1035 | 0.78 | 0.80 | 86 | empty |
| 3 | 57 | 0.24 | 0.71 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–B · 791 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 706 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 94 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 20 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 3ZXB · Wild type single insulin-like growth factor binding domain protein (SIBD-1) from… · the same entry in another collection · chain A against A, TM-score 1.00
- G4V4F9 · AlphaFold monomer V2.0 prediction for single insulin-like growth factor-binding domain… · a predicted model of the same protein · chain B against A, TM-score 0.94
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 G4V4F9
- Elsewhere: RCSB PDB 3ZXB · PDBe 3ZXB · UniProt G4V4F9
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