Research workbench
D-protein rfx-V2 bound to the VEGFR1 domain 3 site on VEGF-a
Analyse D-protein rfx-V2 bound to the VEGFR1 domain 3 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
- 7LL9
- Type
- protein
- Length
- 601 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform L-VEGF189 of vascular endothelial growth factor a; Rfx-V2
- UniProt
- P15692
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Isoform L-VEGF189 of vascular endothelial growth factor a | protein | 96 | 13% helix, 58% strand | P15692 |
| B | Isoform L-VEGF189 of vascular endothelial growth factor a | protein | 99 | 12% helix, 57% strand | P15692 |
| C, D, G, H | Rfx-V2 | protein | 53 | 75% helix, 0% strand | — |
| F | Isoform L-VEGF189 of vascular endothelial growth factor a | protein | 98 | 12% helix, 57% strand | P15692 |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.59 | 0.76 | 47 | empty |
| 2 | 250 | 0.55 | 0.77 | 33 | empty |
| 3 | 249 | 0.52 | 0.76 | 45 | empty |
| 4 | 209 | 0.50 | 0.76 | 37 | empty |
| 5 | 163 | 0.41 | 0.73 | 30 | empty |
Interfaces
14 interfaces between chains.
- A–B · 1497 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1481 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 675 Ų buried · 10 hydrogen bonds · protein-protein
- F–G · 528 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 520 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 212 d-amino, 12 disulfide (D-amino acid, disulfide).
Compared structures
- 7LL9 · D-Protein RFX-V2 Bound to the VEGFR1 Domain 3 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 7LL9 · PDBe 7LL9 · UniProt P15692
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