4LLW: Mutated Pertuzumab Fab heavy chain

Crystal structure of Pertuzumab Clambda Fab with variable domain redesign (VRD2) at 1.95A. Determined by X-ray diffraction at 1.95 Å resolution. Released 29 Jan 2014.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,778
Mol. weight: 95.48 kDa
Released: 29 Jan 2014

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

Secondary structure: helices and β-sheets

4LLW contains 34 α-helices and 85 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.

Chain A: 9 helices, 22 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	44-52	9	2
β-strand	57-60	4	2
β-strand	68-73	6	1
α-helix	74-76	3
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	2
β-strand	106-109	4	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
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	192-194	3
β-strand	200-206	7	5
α-helix	207-209	3
β-strand	211-217	7	5

Chain B: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-13	4	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	62-67	6	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	102-106	5	7
α-helix	112-114	3
β-strand	115-119	5	8
α-helix	120-122	3
α-helix	123-127	5
β-strand	132-139	8	8
β-strand	145-151	7	9
β-strand	154-161	8	9
β-strand	164-165	2	8
β-strand	173-180	8	8
α-helix	183-188	6
β-strand	192-198	7	9
β-strand	201-207	7	9

Chain C: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	11-12	2	11
β-strand	18-25	8	10
α-helix	29-31	3
β-strand	34-40	7	12
β-strand	44-51	8	12
β-strand	58-60	3	12
α-helix	62-64	3
β-strand	68-73	6	10
α-helix	74-76	3
β-strand	78-83	6	10
α-helix	88-90	3
β-strand	92-100	9	12
β-strand	103-109	7	12
β-strand	113-115	3	12
β-strand	116-117	2	11
β-strand	123	1	13
α-helix	124-125	2
β-strand	126-130	5	14
β-strand	141-151	11	14
β-strand	152	1	13
β-strand	157-160	4	15
α-helix	161-163	3
β-strand	169-171	3	14
α-helix	172-174	3
β-strand	175-176	2	14
β-strand	182-191	10	14
α-helix	194-197	4
β-strand	201-206	6	15
α-helix	207-209	3
β-strand	211-216	6	15

Chain D: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	16
β-strand	10-13	4	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	96	1
β-strand	97-98	2	17
β-strand	102-106	5	17
β-strand	111	1	18
α-helix	114	1
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	154-155	2	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

>4LLW_1 mutated Pertuzumab Fab heavy chain (chains A, C)
EVQLVESGGGLVQPGGSLRLSCAASGFTFTDYTMDWVRYAPGKGLEWVADVNPNSGGSIY
NQRFKGRFTLSVDRSKNTLYLQMNSLRAEDTAVYYCARNLGPSFYFDYWGQGTLVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

Sequence of entity 2 (B, D), FASTA

>4LLW_2 light chain Clambda (chains B, D)
DIQMTQSPSSLSASVGDRVTITCKASQDVSIGVAWYQRKPGKAPKLLIYSASYRYTGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQYYIYPYTFGQGTKVEIKGQPKAAPSVTLFP
PSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLS
LTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC

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:

4LLY 1.6 Å, Crystal structure of Pertuzumab Clambda Fab with variable and constant domain redesigns…
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
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

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