Research workbench
Crystal structure of vascular endothelial growth factor-B in complex with a neutralizing antibody Fab fragment
Analyse Crystal structure of vascular endothelial growth factor-B in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VWE
- Type
- protein
- Length
- 1,060 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vascular endothelial growth factor B; Anti-VEGF-B monoclonal antibody
- UniProt
- P49765
- Pockets
- 14 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Vascular endothelial growth factor B | protein | 97 | 8% helix, 56% strand | P49765 |
| C, J | Anti-VEGF-B monoclonal antibody | protein | 214 | 5% helix, 47% strand | — |
| E, L | Anti-VEGF-B monoclonal antibody | protein | 219 | 3% helix, 47% strand | — |
Pockets
14 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.63 | 0.74 | 86 | empty |
| 2 | 304 | 0.55 | 0.76 | 40 | empty |
| 3 | 198 | 0.46 | 0.74 | 33 | empty |
| 4 | 121 | 0.41 | 0.76 | 21 | empty |
| 5 | 50 | 0.37 | 0.80 | 17 | empty |
Interfaces
11 interfaces between chains.
- C–E · 2061 Ų buried · 24 hydrogen bonds · protein-protein
- J–L · 2025 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1488 Ų buried · 14 hydrogen bonds · protein-protein
- B–L · 690 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 666 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 2VWE · Crystal Structure of Vascular Endothelial Growth Factor-B in Complex with a Neutralizing… · the same entry in another collection · chain C against C, TM-score 1.00
- P49765 · AlphaFold monomer V2.0 prediction for vascular endothelial growth factor B (P49765) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P49765
- Elsewhere: RCSB PDB 2VWE · PDBe 2VWE · UniProt P49765
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