MolNFT v1 · #181351 · protein

Structure of B1, a monoclonal VEGFR2 antibody parental of KD035

7LSB · B1 Fab heavy chain: “Structure of B1, a monoclonal VEGFR2 antibody parental of KD035”. X-ray diffraction, 4 pockets (best druggability 0.52). MolNFT v1 #181351 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7LSB
Type: protein
Length: 424 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: B1 Fab heavy chain; B1 Fab light chain
Pockets: 4 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	B1 Fab heavy chain	protein	215	7% helix, 50% strand	—
D	B1 Fab light chain	protein	209	8% helix, 50% strand	—

Pockets

4 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	348	0.52	0.73	48	empty
2	107	0.40	0.76	23	empty
3	68	0.38	0.79	18	empty
4	71	0.32	0.75	16	empty

Interfaces

1 interface between chains.

B–D · 1720 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7LSB · Structure of B1, a monoclonal VEGFR2 antibody parental of KD035 · the same entry in another collection · chain B against B, 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 7LSB · PDBe 7LSB

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