MolNFT v1 · #28948 · protein
Crystal structure of GLY19 deletion mutant of human acidic fibroblast growth factor
1YTO · Heparin-binding growth factor 1: “Crystal structure of GLY19 deletion mutant of human acidic fibroblast growth factor”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.60). MolNFT v1 #28948 on GenesisL1: 3D…
- PDB
- 1YTO
- Type
- protein
- Length
- 559 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heparin-binding growth factor 1
- UniProt
- P05230
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heparin-binding growth factor 1 | protein | 139 | 9% helix, 37% strand | P05230 |
| B, C | Heparin-binding growth factor 1 | protein | 141 | 6% helix, 36% strand | P05230 |
| D | Heparin-binding growth factor 1 | protein | 138 | 7% helix, 40% strand | P05230 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, D, B
- FMT · Formic acid · additive · 3 copies · chains A, C, D
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 | 454 | 0.60 | 0.75 | 50 | empty |
| 2 | 128 | 0.43 | 0.76 | 20 | empty |
| 3 | 117 | 0.39 | 0.75 | 20 | empty |
| 4 | 52 | 0.25 | 0.73 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 439 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 424 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 106 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1YTO · Crystal Structure of Gly19 deletion Mutant 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 D against A, TM-score 0.97
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 1YTO · PDBe 1YTO · UniProt P05230
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