Research workbench
Acidic Fibroblast Growth Factor (FGF-1) complexed with gentisic acid
Analyse Acidic Fibroblast Growth Factor (FGF-1) complexed with gentisic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JUT
- Type
- protein
- Length
- 780 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.25
- Source
- Homo sapiens
- Molecule
- Heparin-binding growth factor 1
- UniProt
- P05230
- Ligands
- GTQ
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · resolution 2.25 · 1 distinct chain · 12% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Heparin-binding growth factor 1 | protein | 130 | 12% helix, 42% strand | P05230 |
Ligands and binding sites
- GTQ · 2,5-dihydroxybenzoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 488 | 0.64 | 0.76 | 52 | empty |
| 2 | 131 | 0.50 | 0.80 | 22 | empty |
| 3 | 177 | 0.47 | 0.75 | 28 | empty |
| 4 | 56 | 0.31 | 0.76 | 17 | empty |
Interfaces
6 interfaces between chains.
- D–E · 605 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 499 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 455 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 239 Ų buried · 1 hydrogen bond · protein-protein
- E–F · 127 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3JUT · Acidic fibroblast growth factor (FGF-1) complexed with gentisic acid · the same entry in another collection · chain F against F, TM-score 1.00
- P05230 · AlphaFold monomer V2.0 prediction for fibroblast growth factor 1 (P05230) · a predicted model of the same protein · chain D 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 P05230
- Elsewhere: RCSB PDB 3JUT · PDBe 3JUT · UniProt P05230
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