Research workbench
Solution structure of a phage-derived peptide antagonist in complex with vascular endothelial growth factor
Analyse Solution structure of a phage-derived peptide antagonist in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KAT
- Type
- protein
- Length
- 236 residues
- Chains
- 4
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vascular endothelial growth factor; Phage-derived peptide antagonist
- UniProt
- P15692
- Pockets
- 3 · best druggability 0.42
Structure
solution nmr · 2 distinct chains · 14% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| V, W | Vascular endothelial growth factor | protein | 99 | 12% helix, 54% strand | P15692 |
| X, Y | Phage-derived peptide antagonist | protein | 19 | 26% helix, 0% strand | — |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.42 | 0.77 | 23 | empty |
| 2 | 81 | 0.35 | 0.76 | 17 | empty |
| 3 | 76 | 0.31 | 0.74 | 16 | empty |
Interfaces
5 interfaces between chains.
- V–W · 1516 Ų buried · 8 hydrogen bonds · protein-protein
- W–X · 434 Ų buried · 5 hydrogen bonds · protein-protein
- V–Y · 423 Ų buried · 3 hydrogen bonds · protein-protein
- W–Y · 155 Ų buried · 2 hydrogen bonds · protein-protein
- V–X · 151 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 1KAT · Solution Structure of a Phage-Derived Peptide Antagonist in Complex with Vascular… · the same entry in another collection · chain V against V, TM-score 1.00
- P15692 · AlphaFold monomer V2.0 prediction for vascular endothelial growth factor a (P15692) · a predicted model of the same protein · chain V 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 P15692
- Elsewhere: RCSB PDB 1KAT · PDBe 1KAT · UniProt P15692
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