6E4Y: Anti-PCSK9 fab 6E2

Anti-PCSK9 fab 6E2 bound to the N-terminal peptide from PCSK9, unmodified. Determined by X-ray diffraction at 2.24 Å resolution. Released 10 Apr 2019.

Method: X-ray diffraction
Resolution: 2.24 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 3,536
Mol. weight: 51.06 kDa
Ligands: ZN
Released: 10 Apr 2019

Explore 6E4Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6E4Y contains 17 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: 9 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	34-40	7	2
β-strand	44-51	8	2
α-helix	52B-53	3
β-strand	57-59	3	2
β-strand	67-72	6	1
α-helix	73-75	3
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-93	6	2
β-strand	103	1	2
β-strand	107-111	5	2
α-helix	114-116	3
β-strand	117	1	3
β-strand	120-124	5	4
β-strand	135-145	11	4
β-strand	146	1	3
β-strand	151-154	4	5
α-helix	155-157	3
β-strand	163-165	3	4
α-helix	166-168	3
β-strand	169-170	2	4
β-strand	176-185	10	4
α-helix	186-188	3
β-strand	189	1	6
β-strand	192	1	6
β-strand	194-200	7	5
α-helix	201-203	3
β-strand	205-211	7	5

Chain L: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	7
β-strand	10-13	4	8
β-strand	19-25	7	7
β-strand	27C	1	9
β-strand	31	1	9
β-strand	33-38	6	8
β-strand	45-49	5	8
β-strand	53-54	2	8
α-helix	55	1
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	84-90	7	8
α-helix	96	1
β-strand	97-98	2	8
β-strand	102-106	5	8
β-strand	111	1	10
β-strand	114-118	5	11
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	11
β-strand	140	1	10
β-strand	145-150	6	12
β-strand	153-154	2	12
β-strand	159-163	5	11
α-helix	164-167	4
β-strand	173-182	10	11
α-helix	183-186	4
β-strand	191-197	7	12
β-strand	205-210	6	12

Chain P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	37-45	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
6E2 heavy chain	H	protein	224	Mus musculus
6E2 light chain	L	protein	219	Mus musculus	A0A097PUG4 (AlphaFold model)
Proprotein convertase subtilisin/kexin type 9	P	protein	22	Homo sapiens	Q8NBP7 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>6E4Y_1 6E2 heavy chain (chains H)
EVKLEESGGGLVQPGGSMKLSCVASRFTLSKYWMNWVRQSPEKGLEWVAQIRLKSDNYAT
HYAESVKGRFTISRDDSKSSVYLQMNNLRAEDTGIYYCTGEIFVNWGQGTLVTVSAASTK
GPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYS
LSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 2 (L), FASTA

>6E4Y_2 6E2 light chain (chains L)
DIVMTQAAPSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLA
SGVPDRFSGSGSGTAFTLRISRVEAEDVGVYYCMQHLEYPFTFGAGTKLELKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (P), FASTA

>6E4Y_3 Proprotein convertase subtilisin/kexin type 9 (chains P)
EDEDGDYEELVLALRSEEDGLA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Water and common crystallization additives (CL) are not listed.

Primary citation

Identification of a Helical Segment within the Intrinsically Disordered Region of the PCSK9 Prodomain. Ultsch, M., Li, W., Eigenbrot, C. et al. J Mol Biol (2019) 431:885-903. DOI 10.1016/j.jmb.2018.11.025 · PubMed

Other PDB entries of the same protein (UniProt A0A097PUG4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6MV5 2.1 Å, Anti-PCSK9 fab 6E2 bound to the N-terminal peptide from PCSK9 (E32K)
6E4Z 2.2 Å, Anti-PCSK9 fab 6E2 bound to the modified N-terminal peptide from PCSK9
1IT9 2.8 Å, Crystal structure of an antigen-binding fragment from a humanized version of the…

Browse structure collections

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