Research workbench
Crystal structure of vegfr-2 domains 4-5 in complex with darpin D4B
Analyse Crystal structure of vegfr-2 domains 4-5 in complex with darpin D4B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OYJ
- Type
- protein
- Length
- 759 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Darpin D4B; Vascular endothelial growth factor receptor 2
- EC
- 2.7.10.1
- UniProt
- P35968
- Ligands
- NAG, GLC, CA, NA
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Darpin D4B | protein | 161 | 52% helix, 0% strand | — |
| B | Darpin D4B | protein | 157 | 54% helix, 0% strand | — |
| C | Vascular endothelial growth factor receptor 2 (EC 2.7.10.1) | protein | 223 | 3% helix, 54% strand | P35968 |
| D | Vascular endothelial growth factor receptor 2 (EC 2.7.10.1) | protein | 218 | 1% helix, 53% strand | P35968 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains C, A, B, D
- GLC · alpha-D-glucopyranose · sugar · 6 copies · chains B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, C, D
- NA · Sodium ion · metal · chains A
- CAC · Cacodylate ion · additive · chains C
- ACT · Acetate ion · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.63 | 0.79 | 30 | empty |
| 2 | 225 | 0.51 | 0.76 | 35 | CA |
| 3 | 57 | 0.44 | 0.83 | 16 | empty |
| 4 | 59 | 0.36 | 0.78 | 19 | ACT |
Interfaces
3 interfaces between chains.
- A–D · 1152 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 412 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 235 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 7 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 5OYJ · Crystal structure of VEGFR-2 domains 4-5 in complex with DARPin D4b · 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 P35968
- Elsewhere: RCSB PDB 5OYJ · PDBe 5OYJ · UniProt P35968
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