Research workbench
D-protein rfx-V1 bound to the VEGFR1 domain 2 site on VEGF-a
Analyse D-protein rfx-V1 bound to the VEGFR1 domain 2 site on VEGF-a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LL8
- Type
- protein
- Length
- 298 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform L-VEGF189 of vascular endothelial growth factor a; Rfx-V1
- UniProt
- P15692
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform L-VEGF189 of vascular endothelial growth factor a | protein | 97 | 15% helix, 62% strand | P15692 |
| B | Isoform L-VEGF189 of vascular endothelial growth factor a | protein | 95 | 13% helix, 64% strand | P15692 |
| C, D | Rfx-V1 | protein | 53 | 79% 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 | 203 | 0.47 | 0.74 | 43 | empty |
| 2 | 84 | 0.33 | 0.74 | 21 | empty |
| 3 | 73 | 0.31 | 0.74 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1358 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 454 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 433 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 426 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 404 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 102 d-amino, 8 disulfide (D-amino acid, disulfide).
Compared structures
- 7LL8 · D-Protein RFX-V1 Bound to the VEGFR1 Domain 2 Site on VEGF-A · 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 7LL8 · PDBe 7LL8 · UniProt P15692
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