6MH2: Herceptin Fab without antigen

Structure of Herceptin Fab without antigen. Determined by X-ray diffraction at 2.8 Å resolution. Released 29 May 2019.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,736
Mol. weight: 96.37 kDa
Released: 29 May 2019

Explore 6MH2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6MH2 contains 29 α-helices and 91 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: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-106	5	2
β-strand	111	1	3
α-helix	112-113	2
β-strand	114-118	5	4
α-helix	122-125	4
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-148	4	5
β-strand	150	1	6
β-strand	153	1	6
β-strand	159-163	5	4
α-helix	164-167	4
β-strand	173-182	10	4
α-helix	183-187	5
β-strand	191-197	7	5
β-strand	205-210	6	5

Chain B: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	34-39	6	8
β-strand	45-52	8	8
β-strand	57-60	4	8
β-strand	65	1	7
β-strand	68-73	6	7
α-helix	74-76	3
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-98	7	8
β-strand	110	1	8
β-strand	114-118	5	8
α-helix	121-123	3
β-strand	124	1	9
α-helix	125-126	2
β-strand	127-131	5	10
β-strand	142-152	11	10
β-strand	153	1	9
β-strand	158-161	4	11
α-helix	162-164	3
β-strand	170-172	3	10
α-helix	173-175	3
β-strand	176-177	2	10
α-helix	178	1
β-strand	183-192	10	10
β-strand	196	1	12
β-strand	199	1	12
β-strand	202-207	6	11
α-helix	208-210	3
β-strand	212-217	6	11

Chain C: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-13	4	14
β-strand	19-25	7	13
β-strand	33-38	6	14
β-strand	44-46	3	14
β-strand	48-49	2	15
β-strand	53-54	2	15
α-helix	55	1
β-strand	62-67	6	13
β-strand	70-75	6	13
α-helix	80-82	3
β-strand	84-90	7	14
α-helix	96	1
β-strand	97-98	2	14
β-strand	102-106	5	14
β-strand	111	1	16
α-helix	112-113	2
β-strand	114-118	5	17
β-strand	131-139	9	17
β-strand	140	1	16
β-strand	145-147	3	18
β-strand	159-163	5	17
α-helix	164-167	4
β-strand	173-180	8	17
α-helix	183-187	5
β-strand	191-197	7	18
β-strand	205-210	6	18

Chain D: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	19
β-strand	10-12	3	20
β-strand	18-25	8	19
α-helix	29-31	3
β-strand	34-39	6	20
β-strand	46-52	7	20
β-strand	57-60	4	20
β-strand	65	1	19
β-strand	68-73	6	19
α-helix	74-76	3
β-strand	78-83	6	19
α-helix	88-90	3
β-strand	92-98	7	20
β-strand	110	1	20
β-strand	114-118	5	20
β-strand	124	1	21
α-helix	125-126	2
β-strand	127-131	5	22
β-strand	146-152	7	22
β-strand	153	1	21
β-strand	158-161	4	23
α-helix	162-164	3
β-strand	171-172	2	22
α-helix	173-175	3
β-strand	176-177	2	22
β-strand	183-188	6	22
β-strand	196	1	24
β-strand	199	1	24
β-strand	201-207	7	23
α-helix	208-210	3
β-strand	212-218	7	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Herceptin Fab arm light chain	A, C	protein	214	Homo sapiens	Q7Z3Y4 (AlphaFold model)
Herceptin Fab arm heavy chain	B, D	protein	231	Homo sapiens

Sequence of entity 1 (A, C), FASTA

>6MH2_1 Herceptin Fab arm light chain (chains A, C)
DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVPS
RFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B, D), FASTA

>6MH2_2 Herceptin Fab arm heavy chain (chains B, D)
EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGLEWVARIYPTNGYTRY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGSHHHHHH

Primary citation

Human Antibody Bispecifics through Phage Display Selection. Luthra, A., Langley, D.B., Schofield, P. et al. Biochemistry (2019) 58:1701-1704. DOI 10.1021/acs.biochem.9b00037 · PubMed

Other PDB entries of the same protein (UniProt Q7Z3Y4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5VSI 1.51 Å, CH1/Ckappa Fab mutant 15.1
6MY4 1.69 Å, Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98M,HC-G99M,LC-S30bR]
6MY5 1.73 Å, Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98F,HC-G99M,LC-S30bR]
4PUB 1.75 Å, Crystal structure of Fab DX-2930
1L7I 1.8 Å, Crystal Structure of the anti-ErbB2 Fab2C4
6MXS 1.95 Å, Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98F,HC-G99M]
6MXR 2.04 Å, Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98M,HC-G99M]
4OGY 2.1 Å, Crystal structure of Fab DX-2930 in complex with human plasma kallikrein at 2.1 Angstrom…
5VR9 2.15 Å, CH1/Ckappa Fab based on Matuzumab
9MY8 2.3 Å, D7 Herpes Virus Simplex Neutralizing Nanobody Bound to HSV Glycoprotein gD
4OGX 2.4 Å, Crystal structure of Fab DX-2930 in complex with human plasma kallikrein at 2.4 Angstrom…
8CWJ 2.45 Å, Fab arms of antibodies 4C12-B12 and CR3022 bound to pangolin receptor binding domain…

Browse structure collections

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