Research workbench
Human fibroblast growth factor-1 (140 amino acid form) with Cys117Val/Pro134Cys mutations
Analyse Human fibroblast growth factor-1 (140 amino acid form) with Cys117Val/Pro134Cys… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NTD
- Type
- protein
- Length
- 569 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.52
- Source
- Homo sapiens
- Molecule
- Acidic fibroblast growth factor 1
- UniProt
- P05230
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · resolution 2.52 · 2 distinct chains · 5% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Acidic fibroblast growth factor 1 | protein | 142 | 4% helix, 39% strand | P05230 |
| B | Acidic fibroblast growth factor 1 | protein | 143 | 6% helix, 37% strand | P05230 |
Ligands and binding sites
- FMT · Formic acid · additive · 11 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 721 | 0.76 | 0.81 | 78 | empty |
| 2 | 168 | 0.61 | 0.83 | 34 | empty |
| 3 | 154 | 0.59 | 0.83 | 29 | empty |
| 4 | 139 | 0.38 | 0.73 | 26 | empty |
| 5 | 74 | 0.33 | 0.74 | 13 | FMT |
Interfaces
5 interfaces between chains.
- A–B · 709 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 704 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 642 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 588 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 201 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2NTD · Human fibroblast growth factor-1 (140 amino acid form) with CYS117VAL/PRO134CYS mutations · 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 0.95
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 2NTD · PDBe 2NTD · UniProt P05230
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