Research workbench
2.0 ångström X-ray structure of human acidic fibroblast growth factor
Analyse 2.0 ångström X-ray structure of human acidic fibroblast growth factor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AFG
- Type
- protein
- Length
- 513 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Homo sapiens
- Molecule
- Acidic fibroblast growth factor
- UniProt
- P05230
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · resolution 2 · 3 distinct chains · 9% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acidic fibroblast growth factor | protein | 129 | 9% helix, 41% strand | P05230 |
| C | Acidic fibroblast growth factor | protein | 127 | 7% helix, 43% strand | P05230 |
| D | Acidic fibroblast growth factor | protein | 128 | 9% helix, 41% strand | P05230 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
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 | 560 | 0.67 | 0.77 | 70 | empty |
| 2 | 326 | 0.58 | 0.77 | 44 | empty |
| 3 | 101 | 0.41 | 0.77 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–D · 372 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 350 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 183 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 162 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 146 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2AFG · 2.0 ångström X-ray structure of human acidic fibroblast growth factor · the same entry in another collection · chain D against D, TM-score 1.00
- P05230 · AlphaFold monomer V2.0 prediction for fibroblast growth factor 1 (P05230) · 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 P05230
- Elsewhere: RCSB PDB 2AFG · PDBe 2AFG · UniProt P05230
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