5EA0: Heavy chain of antibody 7968 Fab fragment

Structure of the antibody 7968 with human complement factor H-derived peptide. Determined by X-ray diffraction at 2.0 Å resolution. Released 25 May 2016.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,721
Mol. weight: 49.36 kDa
Released: 25 May 2016

Explore 5EA0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5EA0 contains 19 α-helices and 46 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	57-59	3	2
β-strand	64	1	1
β-strand	67-72	6	1
α-helix	73-75	3
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-95	8	2
α-helix	96	1
β-strand	100B-105	4	2
β-strand	109-113	5	2
β-strand	119	1	3
α-helix	120-121	2
β-strand	122-126	5	4
β-strand	137-147	11	4
β-strand	148	1	3
β-strand	153-156	4	5
α-helix	157-159	3
β-strand	161	1	5
β-strand	165-167	3	4
α-helix	168-170	3
β-strand	171-172	2	4
β-strand	178-187	10	4
α-helix	188-190	3
β-strand	196-202	7	5
β-strand	207-213	7	5

Chain L: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-14	5	7
β-strand	19-25	7	6
β-strand	27C-27D	2	8
β-strand	30-31	2	8
β-strand	33-38	6	7
β-strand	45-49	5	7
β-strand	53-54	2	7
α-helix	55	1
β-strand	62-67	6	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	84-90	7	7
α-helix	96	1
β-strand	97-98	2	7
β-strand	102-107	6	7
β-strand	111	1	9
α-helix	112-113	2
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	145-150	6	11
β-strand	153-154	2	11
α-helix	155	1
β-strand	159-163	5	10
α-helix	164-167	4
β-strand	173-182	10	10
α-helix	183-188	6
β-strand	191-197	7	11
β-strand	205-210	6	11

Chain P: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1113-1116	4
α-helix	1117-1119	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heavy chain of antibody 7968 Fab fragment	H	protein	224	Homo sapiens
Light chain of antibody 7968 Fab fragment	L	protein	220	Homo sapiens
Complement factor H-related protein 2	P	protein	15	Homo sapiens	P36980 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>5EA0_1 Heavy chain of antibody 7968 Fab fragment (chains H)
EVQLVESGGGVVQPGRSLRLSCAASGFTFSRYGMHWVRQAPGKGLEWVAVMSYDGSTKYY
ADSVKGRFAISRDNPKNTLFLQMNSLRPDDTAVYYCAKGGAAAAVMDVWGKGTTVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

Sequence of entity 2 (L), FASTA

>5EA0_2 Light chain of antibody 7968 Fab fragment (chains L)
DIVMTQSPDSLTVSLGERATISCKSSQRLLYSSNNKNYLAWYQQKPGQPPKLLMYWASTR
ESGVPDRFSGSGSGTDFSLTISSLQAEDVAVYYCQQYYNPPWTFGQGTKVEVKRTVAAPS
VFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYS
LSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (P), FASTA

>5EA0_3 Complement factor H-related protein 2 (chains P)
XGPPPPIDNGDITSX

Primary citation

A Therapeutic Antibody for Cancer, Derived from Single Human B Cells. Bushey, R.T., Moody, M.A., Nicely, N.L. et al. Cell Rep (2016) 15:1505-1513. DOI 10.1016/j.celrep.2016.04.038 · PubMed

Other PDB entries of the same protein (UniProt P36980 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3ZD1 2.0 Å, Structure of the two C-terminal domains of complement factor H related protein 2
9N1Z 2.31 Å, Structure of C3d Bound to a Fragment of FHR-2
9N20 3.3 Å, Structure of C3d Bound to a Fragment of FHR-2 and S. aureus Efb-C

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