Research workbench
Structural basis for the function of two anti-VEGF receptor antibodies
Analyse Structural basis for the function of two anti-VEGF receptor antibodies in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S35
- Type
- protein
- Length
- 540 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6.64 Fab heavy chain; 6.64 Fab light chain; Vascular endothelial growth factor receptor 2
- EC
- 2.7.10.1
- UniProt
- P35968
- Ligands
- NAG, CA
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | 6.64 Fab heavy chain | protein | 211 | 7% helix, 54% strand | — |
| L | 6.64 Fab light chain | protein | 217 | 6% helix, 52% strand | — |
| X | Vascular endothelial growth factor receptor 2 (EC 2.7.10.1) | protein | 112 | 6% helix, 56% strand | P35968 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains L, X
- CA · Calcium ion · metal · 6 copies · chains H, X, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.67 | 0.91 | 30 | CA |
| 2 | 191 | 0.49 | 0.76 | 39 | empty |
| 3 | 61 | 0.36 | 0.79 | 19 | empty |
| 4 | 91 | 0.34 | 0.74 | 17 | empty |
| 5 | 58 | 0.29 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1673 Ų buried · 12 hydrogen bonds · protein-protein
- H–X · 692 Ų buried · 11 hydrogen bonds · protein-protein
- L–X · 514 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3S35 · Structural basis for the function of two anti-VEGF receptor antibodies · the same entry in another collection · chain H against H, 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 3S35 · PDBe 3S35 · UniProt P35968
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