Research workbench
Crystal structure of VEGF-C in complex with domains 2 and 3 of VEGFR2 in a tetragonal crystal form
Analyse Crystal structure of VEGF-C in complex with domains 2 and 3 of VEGFR2 in a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X1X
- Type
- protein
- Length
- 304 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vascular endothelial growth factor C; Vascular endothelial growth factor receptor 2
- UniProt
- P49767, P35968
- Ligands
- NAG, BMA, HG
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Vascular endothelial growth factor C | protein | 103 | 20% helix, 54% strand | P49767 |
| R | Vascular endothelial growth factor receptor 2 | protein | 201 | 3% helix, 53% strand | P35968 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains E, R
- BMA · beta-D-mannopyranose · sugar · 2 copies
- HG · Mercury (II) ion · metal · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.60 | 0.78 | 56 | empty |
| 2 | 58 | 0.30 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- E–R · 657 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 2X1X · Crystal structure of VEGF-C in complex with domains 2 and 3 of VEGFR2 in a tetragonal… · the same entry in another collection · chain E against E, TM-score 1.00
- P49767 · AlphaFold monomer V2.0 prediction for vascular endothelial growth factor C (P49767) · a predicted model of the same protein · chain E against A, TM-score 0.95
- P35968 · AlphaFold monomer V2.0 prediction for vascular endothelial growth factor receptor 2… · a predicted model of the same protein · chain R against A, TM-score 0.92
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 P49767
- Every structure of UniProt P35968
- Elsewhere: RCSB PDB 2X1X · PDBe 2X1X · UniProt P49767 · UniProt P35968
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