Research workbench
Crystal structure of VEGF-C in complex with domains 2 and 3 of VEGFR2
Analyse Crystal structure of VEGF-C in complex with domains 2 and 3 of VEGFR2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X1W
- Type
- protein
- Length
- 1,154 residues
- Chains
- 8
- 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, CS
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 8 distinct chains · 7% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vascular endothelial growth factor C | protein | 98 | 13% helix, 53% strand | P49767 |
| B | Vascular endothelial growth factor C | protein | 98 | 14% helix, 57% strand | P49767 |
| C | Vascular endothelial growth factor C | protein | 97 | 14% helix, 58% strand | P49767 |
| D | Vascular endothelial growth factor C | protein | 99 | 16% helix, 57% strand | P49767 |
| L | Vascular endothelial growth factor receptor 2 | protein | 196 | 3% helix, 53% strand | P35968 |
| M | Vascular endothelial growth factor receptor 2 | protein | 179 | 3% helix, 53% strand | P35968 |
| N | Vascular endothelial growth factor receptor 2 | protein | 194 | 3% helix, 54% strand | P35968 |
| O | Vascular endothelial growth factor receptor 2 | protein | 193 | 3% helix, 54% strand | P35968 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 33 copies · chains A, B, C, D, L, M, N, O
- BMA · beta-D-mannopyranose · sugar · 9 copies · chains O
- CS · Cesium ion · metal · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 698 | 0.75 | 0.81 | 67 | empty |
| 2 | 466 | 0.72 | 0.82 | 51 | CS |
| 3 | 406 | 0.70 | 0.81 | 40 | empty |
| 4 | 366 | 0.64 | 0.79 | 41 | CS |
| 5 | 517 | 0.64 | 0.76 | 69 | empty |
Interfaces
14 interfaces between chains.
- A–B · 1153 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1109 Ų buried · 7 hydrogen bonds · protein-protein
- D–O · 682 Ų buried · 5 hydrogen bonds · protein-protein
- D–L · 675 Ų buried · 5 hydrogen bonds · protein-protein
- A–N · 668 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 20 glycan (disulfide, N-glycosylation).
Compared structures
- 2X1W · Crystal Structure of VEGF-C in Complex with Domains 2 and 3 of VEGFR2 · the same entry in another collection · chain O against O, 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 D against A, TM-score 0.96
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 2X1W · PDBe 2X1W · UniProt P49767 · UniProt P35968
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