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Crystal structure of VEGF in complex with heterodimeric fcab JANUSCT6

Analyse Crystal structure of VEGF in complex with heterodimeric fcab JANUSCT6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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.

Pocket	Volume (Å³)	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 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1181 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 1179 Å² buried · 6 hydrogen bonds · protein-protein
B–F · 594 Å² buried · 3 hydrogen bonds · protein-protein
D–E · 542 Å² 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

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Every structure of UniProt P0DOX5
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Elsewhere: RCSB PDB 5O4E · PDBe 5O4E · UniProt P0DOX5 · UniProt P15692

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