4LLY: Mutated Pertuzumab Fab heavy chain

Crystal structure of Pertuzumab Clambda Fab with variable and constant domain redesigns (VRD2 and CRD2) at 1.6A. Determined by X-ray diffraction at 1.6 Å resolution. Released 29 Jan 2014.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,089
Mol. weight: 94.67 kDa
Ligands: MG
Released: 29 Jan 2014

Explore 4LLY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4LLY contains 42 α-helices and 90 β-strands across 4 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.

Chains A and C: 11 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	33-39	7	2
β-strand	45-51	7	2
β-strand	58-60	3	2
α-helix	62-64	3
β-strand	68-73	6	1
α-helix	74-76	3
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-100	9	2
β-strand	103-109	7	2
β-strand	113-117	5	2
α-helix	121-122	2
β-strand	123	1	3
α-helix	124-125	2
β-strand	126-130	5	4
α-helix	134-136	3
β-strand	137-138	2	4
β-strand	141-151	11	4
β-strand	152	1	3
β-strand	157-160	4	5
α-helix	161-163	3
β-strand	165	1	5
β-strand	169-171	3	4
α-helix	172-174	3
β-strand	175-176	2	4
β-strand	182-191	10	4
α-helix	194-197	4
β-strand	201-206	6	5
α-helix	207-209	3
β-strand	211-216	6	5

Chain B: 10 helices, 22 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	33-38	6	7
β-strand	45-49	5	7
β-strand	53-54	2	7
α-helix	55	1
β-strand	62-66	5	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	84-90	7	7
α-helix	97	1
β-strand	98	1	7
α-helix	99	1
β-strand	102-107	6	7
α-helix	109-111	3
β-strand	112	1	8
α-helix	113-114	2
β-strand	115-119	5	9
α-helix	120-122	3
α-helix	123-127	5
β-strand	131-140	10	9
β-strand	141	1	8
β-strand	146-151	6	10
β-strand	154-156	3	10
β-strand	160-162	3	9
α-helix	163-165	3
β-strand	166-167	2	9
β-strand	173-181	9	9
α-helix	183-188	6
β-strand	192-198	7	10
β-strand	201-207	7	10

Chain D: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	16
β-strand	10-14	5	17
β-strand	19-25	7	16
β-strand	33-38	6	17
β-strand	45-49	5	17
β-strand	53-54	2	17
α-helix	55	1
β-strand	62-67	6	16
β-strand	70-75	6	16
α-helix	80-82	3
β-strand	84-90	7	17
α-helix	97	1
β-strand	98	1	17
α-helix	99	1
β-strand	102-107	6	17
α-helix	109-111	3
β-strand	112	1	18
α-helix	113-114	2
β-strand	115-119	5	19
α-helix	120-122	3
α-helix	123-127	5
β-strand	131-140	10	19
β-strand	141	1	18
β-strand	146-151	6	20
β-strand	154-156	3	20
β-strand	160-162	3	19
α-helix	163-165	3
β-strand	166-167	2	19
β-strand	173-181	9	19
α-helix	183-188	6
β-strand	192-198	7	20
β-strand	201-207	7	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
mutated Pertuzumab Fab heavy chain	A, C	protein	226	Homo sapiens	S6B291 (AlphaFold model)
light chain Clambda	B, D	protein	212	Homo sapiens	P0DOY2 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4LLY_1 mutated Pertuzumab Fab heavy chain (chains A, C)
EVQLVESGGGLVQPGGSLRLSCAASGFTFTDYTMDWVRKAPGKGLEWVADVNPNSGGSIY
NQEFKGRFTLSVDRSKNTLYLQMNSLRAEDTAVYYCARNLGPSFYFDYWGQGTLVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVATGPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

Sequence of entity 2 (B, D), FASTA

>4LLY_2 light chain Clambda (chains B, D)
RIQMTQSPSSLSASVGDRVTITCKASQDVSIGVAWYQDKPGKAPKLLIYSASYRYTGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQYYIYPYTFGQGTKVEIKGQPKAAPSVTLFP
PSSEELQANKATLVCYISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAAWSYLS
LTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

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

Primary citation

Generation of bispecific IgG antibodies by structure-based design of an orthogonal Fab interface. Lewis, S.M., Wu, X., Pustilnik, A. et al. Nat Biotechnol (2014) 32:191-198. DOI 10.1038/nbt.2797 · PubMed

Other PDB entries of the same protein (UniProt S6B291 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3MNZ 1.8 Å, Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment with a gp41…
6B9Z 1.82 Å, Trastuzumab Fab v3
4LLW 1.95 Å, Crystal structure of Pertuzumab Clambda Fab with variable domain redesign (VRD2) at 1.95A
6BAE 2.14 Å, Trastuzumab Fab v3 in complex with CQFDLSTRRLKC
3MNW 2.2 Å, Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment with a gp41…
5VEB 2.34 Å, Crystal structure of a Fab binding to extracellular domain 5 of Cadherin-6
6AZK 2.48 Å, Structure of cetuximab with aminoheptanoic acid-linked N-(3-hydroxypropyl)-L-arginine…
6AYN 2.48 Å, Structure of cetuximab with aminoheptanoic acid-linked N-(3-aminopropyl)-L-arginine…
6AZL 2.48 Å, Structure of cetuximab with aminoheptanoic acid-linked N-carboxyethylarginine meditope…
6AU5 2.48 Å, Structure of cetuximab with aminoheptanoic acid-linked n-butylarginine meditope variant
6AXP 2.48 Å, Structure of cetuximab with aminoheptanoic acid-linked n-octylarginine meditope variant
6VTU 2.61 Å, DH717.1 Fab monomer in complex with man9 glycan

Browse structure collections

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