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Vascular endothelial growth factor in complex with an affinity matured antibody

Analyse Vascular endothelial growth factor in complex with an affinity matured antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1CZ8
Type: protein
Length: 1,050 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vascular endothelial growth factor a; Light chain of neutralizing antibody; Heavy chain…
UniProt: P15692
Ligands: SO4
Pockets: 9 · best druggability 0.63

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
V, W	Vascular endothelial growth factor a	protein	94	13% helix, 64% strand	P15692
L, X	Light chain of neutralizing antibody	protein	213	6% helix, 52% strand	—
H, Y	Heavy chain of neutralizing antibody	protein	218	10% helix, 51% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains W, H, V, Y

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 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	628	0.63	0.74	60	empty
2	188	0.51	0.77	28	empty
3	232	0.50	0.75	29	empty
4	179	0.46	0.75	32	empty
5	103	0.34	0.73	23	empty

Interfaces

9 interfaces between chains.

L–H · 1738 Å² buried · 21 hydrogen bonds · protein-protein
X–Y · 1707 Å² buried · 15 hydrogen bonds · protein-protein
V–W · 1350 Å² buried · 16 hydrogen bonds · protein-protein
V–Y · 834 Å² buried · 22 hydrogen bonds · protein-protein
W–H · 828 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

1CZ8 · Vascular endothelial growth factor in complex with an affinity matured antibody · the same entry in another collection · chain L against L, TM-score 1.00
P15692 · AlphaFold monomer V2.0 prediction for vascular endothelial growth factor a (P15692) · a predicted model of the same protein · chain V against A, TM-score 0.96

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 1CZ8 · PDBe 1CZ8 · UniProt P15692

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