Research workbench
The development of peptide-based tools for the analysis of angiogenesis
Analyse The development of peptide-based tools for the analysis of angiogenesis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S1K
- Type
- protein
- Length
- 292 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Z-domain; Vascular endothelial growth factor a
- UniProt
- P15692
- Pockets
- 2 · best druggability 0.43
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Z-domain | protein | 52 | 81% helix, 0% strand | — |
| V | Vascular endothelial growth factor a | protein | 95 | 13% helix, 61% strand | P15692 |
| W | Vascular endothelial growth factor a | protein | 93 | 16% helix, 60% strand | P15692 |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.43 | 0.74 | 34 | empty |
| 2 | 117 | 0.38 | 0.74 | 23 | empty |
Interfaces
5 interfaces between chains.
- V–W · 1343 Ų buried · 12 hydrogen bonds · protein-protein
- B–V · 578 Ų buried · 6 hydrogen bonds · protein-protein
- A–W · 554 Ų buried · 4 hydrogen bonds · protein-protein
- A–V · 299 Ų buried · 4 hydrogen bonds · protein-protein
- B–W · 285 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3S1K · The Development of Peptide-based Tools for the Analysis of Angiogenesis · the same entry in another collection · chain A against A, TM-score 1.00
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 P15692
- Elsewhere: RCSB PDB 3S1K · PDBe 3S1K · UniProt P15692
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