Research workbench
A complex between acidic fibroblast growth factor and 5-amino-2- naphthalenesulfonate
Analyse A complex between acidic fibroblast growth factor and 5-amino-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HKN
- Type
- protein
- Length
- 772 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heparin-binding growth factor 1
- UniProt
- P05230
- Ligands
- N2M
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F | Heparin-binding growth factor 1 | protein | 128 | 9% helix, 41% strand | P05230 |
| C | Heparin-binding growth factor 1 | protein | 129 | 12% helix, 43% strand | P05230 |
| D | Heparin-binding growth factor 1 | protein | 129 | 14% helix, 40% strand | P05230 |
| E | Heparin-binding growth factor 1 | protein | 130 | 9% helix, 39% strand | P05230 |
Ligands and binding sites
- N2M · 5-amino-naphtalene-2-monosulfonate · ligand · 2 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.75 | 0.88 | 40 | empty |
| 2 | 296 | 0.69 | 0.83 | 45 | empty |
| 3 | 60 | 0.46 | 0.84 | 21 | empty |
| 4 | 218 | 0.45 | 0.73 | 26 | empty |
| 5 | 168 | 0.43 | 0.74 | 31 | empty |
Interfaces
7 interfaces between chains.
- D–F · 639 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 620 Ų buried · 4 hydrogen bonds · protein-protein
- A–F · 567 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 552 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 374 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1HKN · A complex between acidic fibroblast growth factor and 5-amino-2-naphthalenesulfonate · 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 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 1HKN · PDBe 1HKN · UniProt P05230
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