Research workbench
Crystal structure of plgf in complex with domain 2 of VEGFR1
Analyse Crystal structure of plgf in complex with domain 2 of VEGFR1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RV6
- Type
- protein
- Length
- 373 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Placenta growth factor (plgf); FLT1 protein
- UniProt
- P49763, P17948
- Pockets
- 4 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| V | Placenta growth factor (plgf) | protein | 94 | 13% helix, 59% strand | P49763 |
| W | Placenta growth factor (plgf) | protein | 95 | 16% helix, 58% strand | P49763 |
| X, Y | FLT1 protein | protein | 92 | 3% helix, 47% strand | P17948 |
Ligands and binding sites
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains V, W, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.47 | 0.81 | 22 | empty |
| 2 | 75 | 0.44 | 0.81 | 17 | empty |
| 3 | 88 | 0.43 | 0.79 | 22 | empty |
| 4 | 79 | 0.39 | 0.78 | 18 | empty |
Interfaces
5 interfaces between chains.
- V–W · 1285 Ų buried · 12 hydrogen bonds · protein-protein
- W–X · 633 Ų buried · 6 hydrogen bonds · protein-protein
- V–Y · 606 Ų buried · 4 hydrogen bonds · protein-protein
- W–Y · 296 Ų buried · 0 hydrogen bonds · protein-protein
- V–X · 295 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 1RV6 · Crystal Structure of PlGF in Complex with Domain 2 of VEGFR1 · the same entry in another collection · chain V against V, TM-score 1.00
- P17948 · AlphaFold monomer V2.0 prediction for vascular endothelial growth factor receptor 1… · a predicted model of the same protein · chain X against A, TM-score 0.98
- P49763 · AlphaFold monomer V2.0 prediction for placenta growth factor (P49763) · a predicted model of the same protein · chain V against A, TM-score 0.91
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 P49763
- Every structure of UniProt P17948
- Elsewhere: RCSB PDB 1RV6 · PDBe 1RV6 · UniProt P49763 · UniProt P17948
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