MolNFT v1 · #179754 · protein

Crystal structure of BH1 Fab variant (cdr H3 loop design 14_0130) in complex with VEGF

7KF1 · Anti-VEGF-a Fab BH1 heavy chain: “Crystal structure of BH1 Fab variant (cdr H3 loop design 14_0130) in complex with VEGF”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.65). MolNFT v1 #179754 on GenesisL1: 3D…

PDB: 7KF1
Type: protein
Length: 2,118 residues
Chains: 12
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: 20 · best druggability 0.65

Structure

x-ray diffraction · 8 distinct chains · 8% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Anti-VEGF-a Fab BH1 heavy chain	protein	225	9% helix, 52% strand	—
L, E, I	Anti-VEGF-a Fab BH1 light chain	protein	217	6% helix, 51% strand	—
V, F	Isoform L-VEGF206 of vascular endothelial growth factor a	protein	95	13% helix, 62% strand	—
A	Anti-VEGF-a Fab BH1 heavy chain	protein	215	8% helix, 52% strand	—
B	Anti-VEGF-a Fab BH1 light chain	protein	216	6% helix, 51% strand	—
C, J	Isoform L-VEGF206 of vascular endothelial growth factor a	protein	94	13% helix, 63% strand	—
D	Anti-VEGF-a Fab BH1 heavy chain	protein	216	8% helix, 53% strand	—
G	Anti-VEGF-a Fab BH1 heavy chain	protein	217	8% helix, 53% strand	—

Ligands and binding sites

CL · Chloride ion · ion · 12 copies · chains H, L, A, B, D, E, G, I

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	574	0.65	0.76	74	empty
2	452	0.63	0.77	71	empty
3	614	0.63	0.74	67	empty
4	329	0.60	0.78	40	empty
5	341	0.59	0.77	50	empty

Interfaces

15 interfaces between chains.

H–L · 1842 Å² buried · 15 hydrogen bonds · protein-protein
G–I · 1765 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1737 Å² buried · 17 hydrogen bonds · protein-protein
D–E · 1718 Å² buried · 15 hydrogen bonds · protein-protein
B–I · 1006 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 28 disulfide (disulfide).

Compared structures

7KF1 · Crystal structure of bH1 Fab variant (CDR H3 loop design 14_0130) 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 7KF1 · PDBe 7KF1

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