Research workbench
The FGF1-S100A13-C2A hetero-hexameric complex structure: a component in the non-classical pathway for FGF1 secretion
Analyse The FGF1-S100A13-C2A hetero-hexameric complex structure: a component in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2KI6
- Type
- protein
- Length
- 718 residues
- Chains
- 6
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Synaptotagmin-1; Heparin-binding growth factor 1; Protein S100-A13
- UniProt
- P21579, P05230, Q99584
- Pockets
- 14 · best druggability 0.78
Structure
solution nmr · 3 distinct chains · 20% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Synaptotagmin-1 | protein | 128 | 5% helix, 47% strand | P21579 |
| B, E | Heparin-binding growth factor 1 | protein | 133 | 10% helix, 33% strand | P05230 |
| C, D | Protein S100-A13 | protein | 98 | 54% helix, 4% strand | Q99584 |
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 804 | 0.78 | 0.81 | 62 | empty |
| 2 | 52 | 0.73 | 0.99 | 21 | empty |
| 3 | 52 | 0.68 | 0.96 | 17 | empty |
| 4 | 407 | 0.67 | 0.80 | 53 | empty |
| 5 | 303 | 0.60 | 0.78 | 49 | empty |
Interfaces
9 interfaces between chains.
- C–D · 960 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 550 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 516 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 463 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 382 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 d-amino (D-amino acid).
Compared structures
- 2KI6 · The FGF1-S100A13-C2A hetero-hexameric complex structure: A component in the non-classical… · the same entry in another collection · chain F against F, TM-score 1.00
- P21579 · AlphaFold monomer V2.0 prediction for synaptotagmin-1 (P21579) · a predicted model of the same protein · chain A against A, TM-score 0.90
- P05230 · AlphaFold monomer V2.0 prediction for fibroblast growth factor 1 (P05230) · a predicted model of the same protein · chain E against A, TM-score 0.82
- Q99584 · AlphaFold monomer V2.0 prediction for protein S100-A13 (Q99584) · a predicted model of the same protein · chain C against A, TM-score 0.81
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 P21579
- Every structure of UniProt P05230
- Every structure of UniProt Q99584
- Elsewhere: RCSB PDB 2KI6 · PDBe 2KI6 · UniProt P21579 · UniProt P05230 · UniProt Q99584
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