MolNFT v1 · #179753 · protein

Crystal structure of BH1 Fab variant (cdr H3 loop design 13_0346) in complex with VEGF

7KF0 · Anti-VEGF-a Fab BH1 heavy chain: “Crystal structure of BH1 Fab variant (cdr H3 loop design 13_0346) in complex with VEGF”. X-ray diffraction, 1 ligand (CL), 11 pockets (best druggability 0.61). MolNFT v1 #179753 on GenesisL1: 3D…

PDB: 7KF0
Type: protein
Length: 1,058 residues
Chains: 6
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: 11 · best druggability 0.61

Structure

x-ray diffraction · 4 distinct chains · 8% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Anti-VEGF-a Fab BH1 heavy chain	protein	215	8% helix, 50% strand	—
L, B	Anti-VEGF-a Fab BH1 light chain	protein	216	6% helix, 52% strand	—
V, C	Isoform L-VEGF206 of vascular endothelial growth factor a	protein	95	13% helix, 64% strand	—
A	Anti-VEGF-a Fab BH1 heavy chain	protein	221	8% helix, 50% strand	—

Ligands and binding sites

CL · Chloride ion · ion · chains A
EDO · 1,2-ethanediol · additive · 2 copies · chains L, B

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

Pockets

11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	553	0.61	0.74	61	empty
2	524	0.60	0.74	54	empty
3	51	0.53	0.89	20	empty
4	96	0.41	0.77	18	empty
5	122	0.40	0.75	27	empty

Interfaces

11 interfaces between chains.

A–B · 1839 Å² buried · 18 hydrogen bonds · protein-protein
H–L · 1772 Å² buried · 16 hydrogen bonds · protein-protein
V–C · 1427 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 499 Å² buried · 11 hydrogen bonds · protein-protein
L–V · 489 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

7KF0 · Crystal structure of bH1 Fab variant (CDR H3 loop design 13_0346) 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 7KF0 · PDBe 7KF0

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