Research workbench
Structural basis for the inhibition of insulin-like growth factors by igf binding proteins
Analyse Structural basis for the inhibition of insulin-like growth factors by igf… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DSQ
- Type
- protein
- Length
- 409 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin-like growth factor-binding protein 4; Insulin-like growth factor ib; Insulin-like…
- UniProt
- P22692, P05019, P08833
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 27% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Insulin-like growth factor-binding protein 4 | protein | 87 | 20% helix, 23% strand | P22692 |
| I | Insulin-like growth factor ib | protein | 49 | 53% helix, 4% strand | P05019 |
| A | Insulin-like growth factor-binding protein 4 | protein | 91 | 15% helix, 23% strand | P22692 |
| C | Insulin-like growth factor ib | protein | 51 | 53% helix, 8% strand | P05019 |
| G | Insulin-like growth factor-binding protein 1 | protein | 73 | 21% helix, 23% strand | P08833 |
| H | Insulin-like growth factor-binding protein 1 | protein | 58 | 21% helix, 17% strand | P08833 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 516 | 0.71 | 0.80 | 53 | empty |
| 2 | 288 | 0.55 | 0.76 | 35 | empty |
| 3 | 82 | 0.51 | 0.84 | 25 | empty |
| 4 | 146 | 0.42 | 0.75 | 17 | empty |
| 5 | 133 | 0.38 | 0.73 | 24 | empty |
Interfaces
8 interfaces between chains.
- A–C · 911 Ų buried · 11 hydrogen bonds · protein-protein
- B–I · 911 Ų buried · 8 hydrogen bonds · protein-protein
- I–G · 695 Ų buried · 4 hydrogen bonds · protein-protein
- A–G · 566 Ų buried · 2 hydrogen bonds · protein-protein
- C–H · 561 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 23 disulfide (disulfide).
Compared structures
- 2DSQ · Structural Basis for the Inhibition of Insulin-like Growth Factors by IGF Binding Proteins · the same entry in another collection · chain H against H, TM-score 1.00
- P22692 · AlphaFold monomer V2.0 prediction for insulin-like growth factor- binding protein 4… · a predicted model of the same protein · chain B against A, TM-score 0.98
- P08833 · AlphaFold monomer V2.0 prediction for insulin-like growth factor- binding protein 1… · a predicted model of the same protein · chain H against A, TM-score 0.95
- P05019 · AlphaFold monomer V2.0 prediction for insulin-like growth factor I (P05019) · a predicted model of the same protein · chain I against A, TM-score 0.84
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 P22692
- Every structure of UniProt P05019
- Every structure of UniProt P08833
- Elsewhere: RCSB PDB 2DSQ · PDBe 2DSQ · UniProt P22692 · UniProt P05019 · UniProt P08833
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