MolNFT v1 · #128901 · protein
Crystal structure of VEGF in complex with heterodimeric fcab JANUSCT6
5O4E · Immunoglobulin gamma-1 heavy chain: “Crystal structure of VEGF in complex with heterodimeric fcab JANUSCT6”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 7 pockets (best druggability 0.51). MolNFT v1 #128901 on GenesisL1: 3D…
- PDB
- 5O4E
- Type
- protein
- Length
- 1,010 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin gamma-1 heavy chain; Vascular endothelial growth factor a
- UniProt
- P0DOX5, P15692
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 7 · best druggability 0.51
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Immunoglobulin gamma-1 heavy chain | protein | 209 | 11% helix, 47% strand | P0DOX5 |
| B | Immunoglobulin gamma-1 heavy chain | protein | 216 | 11% helix, 47% strand | P0DOX5 |
| C | Immunoglobulin gamma-1 heavy chain | protein | 181 | 12% helix, 48% strand | P0DOX5 |
| D | Immunoglobulin gamma-1 heavy chain | protein | 214 | 11% helix, 47% strand | P0DOX5 |
| E, F | Vascular endothelial growth factor a | protein | 95 | 13% helix, 64% strand | P15692 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, B, D
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 10 copies · chains A, B, C, D, E, F
- CAC · Cacodylate ion · additive · 2 copies · chains A, E
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 267 | 0.51 | 0.74 | 47 | empty |
| 2 | 262 | 0.50 | 0.74 | 36 | empty |
| 3 | 238 | 0.48 | 0.74 | 31 | empty |
| 4 | 84 | 0.33 | 0.75 | 21 | empty |
| 5 | 58 | 0.32 | 0.76 | 19 | empty |
Interfaces
7 interfaces between chains.
- E–F · 1412 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1181 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1179 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 594 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 542 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5O4E · Crystal structure of VEGF in complex with heterodimeric Fcab JanusCT6 · 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 P0DOX5
- Every structure of UniProt P15692
- Elsewhere: RCSB PDB 5O4E · PDBe 5O4E · UniProt P0DOX5 · UniProt P15692
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