Research workbench

Crystal structure of BH1 Fab variant (cdr H3 loop design 16_0325) in complex with VEGF

Analyse Crystal structure of BH1 Fab variant (cdr H3 loop design 16_0325) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7KEZ
Type: protein
Length: 530 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Anti-VEGF-a Fab BH1 heavy chain; Anti-VEGF-a Fab BH1 light chain; Isoform L-VEGF206 of…
Ligands: CL
Pockets: 5 · best druggability 0.61

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Anti-VEGF-a Fab BH1 heavy chain	protein	220	8% helix, 52% strand	—
L	Anti-VEGF-a Fab BH1 light chain	protein	216	6% helix, 52% strand	—
V	Isoform L-VEGF206 of vascular endothelial growth factor a	protein	94	13% helix, 61% strand	—

Ligands and binding sites

CL · Chloride ion · ion · chains H

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

Pockets

5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	589	0.61	0.73	60	empty
2	127	0.42	0.76	24	empty
3	83	0.35	0.75	18	empty
4	97	0.34	0.74	24	empty
5	53	0.30	0.76	14	empty

Interfaces

3 interfaces between chains.

H–L · 1842 Å² buried · 17 hydrogen bonds · protein-protein
L–V · 476 Å² buried · 11 hydrogen bonds · protein-protein
H–V · 376 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

7KEZ · Crystal structure of bH1 Fab variant (CDR H3 loop design 16_0325) in complex with VEGF · the same entry in another collection · chain H against H, 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
Elsewhere: RCSB PDB 7KEZ · PDBe 7KEZ

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.