Research workbench
Structure of VEGF complexed to a Fab containing tyr and ser in the cdrs
Analyse Structure of VEGF complexed to a Fab containing tyr and ser in the cdrs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QR0
- Type
- protein
- Length
- 4,200 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab-fragment light chain; Fab-fragment heavy chain; Vascular endothelial growth factor a
- UniProt
- P15692
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, G, K, M, Q, S, W | Fab-fragment light chain | protein | 213 | 6% helix, 51% strand | — |
| B, F, H, L, N, R, T, X | Fab-fragment heavy chain | protein | 216 | 6% helix, 54% strand | — |
| C, I, O, U | Vascular endothelial growth factor a | protein | 95 | 12% helix, 61% strand | P15692 |
| D, J, P, V | Vascular endothelial growth factor a | protein | 97 | 11% helix, 60% strand | P15692 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 998 | 0.69 | 0.74 | 114 | empty |
| 2 | 607 | 0.64 | 0.75 | 51 | empty |
| 3 | 434 | 0.62 | 0.77 | 45 | empty |
| 4 | 594 | 0.61 | 0.73 | 56 | empty |
| 5 | 397 | 0.61 | 0.76 | 55 | empty |
Interfaces
48 interfaces between chains.
- Q–R · 1882 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1860 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 1841 Ų buried · 16 hydrogen bonds · protein-protein
- W–X · 1826 Ų buried · 14 hydrogen bonds · protein-protein
- S–T · 1824 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 64 disulfide (disulfide).
Compared structures
- 2QR0 · Structure of VEGF complexed to a Fab containing TYR and SER in the CDRs · the same entry in another collection · chain J against J, 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 2QR0 · PDBe 2QR0 · UniProt P15692
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