4EOW: MB007 human IgG1 Fab fragment heavy chain

Crystal structure of a disease-associated anti-human GM-CSF autoantibody MB007. Determined by X-ray diffraction at 1.97 Å resolution. Released 22 Aug 2012.

Method: X-ray diffraction
Resolution: 1.97 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,626
Mol. weight: 47.54 kDa
Released: 22 Aug 2012

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

Secondary structure: helices and β-sheets

4EOW contains 15 α-helices and 47 β-strands across 2 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, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-25	8	1
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	58-60	3	2
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-98	7	2
α-helix	106-111	6
β-strand	117	1	2
β-strand	121-125	5	2
β-strand	131	1	3
α-helix	132-133	2
β-strand	134-141	8	4
β-strand	149-159	11	4
β-strand	160	1	3
β-strand	165-168	4	5
α-helix	169-171	3
β-strand	173	1	5
β-strand	177-179	3	4
α-helix	180-182	3
β-strand	183-184	2	4
β-strand	190-199	10	4
α-helix	200-202	3
β-strand	203	1	6
β-strand	206	1	6
β-strand	209-214	6	5
α-helix	215-217	3
β-strand	219-224	6	5

Chain L: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	7
β-strand	9-12	4	8
β-strand	18-23	6	7
β-strand	35-39	5	8
β-strand	46-49	4	8
β-strand	50	1	9
β-strand	54	1	9
α-helix	55-56	2
β-strand	63-67	5	7
β-strand	71-76	6	7
α-helix	81-83	3
β-strand	85-93	9	8
β-strand	98-101	4	8
β-strand	105-109	5	8
β-strand	115	1	10
α-helix	116-117	2
β-strand	118-122	5	11
α-helix	123-125	3
α-helix	126-130	5
β-strand	134-143	10	11
β-strand	144	1	10
β-strand	149-154	6	12
β-strand	157-159	3	12
β-strand	163-165	3	11
α-helix	166-168	3
β-strand	169-170	2	11
β-strand	176-184	9	11
α-helix	186-191	6
β-strand	195-201	7	12
β-strand	204-210	7	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MB007 human IgG1 Fab fragment heavy chain	H	protein	228	Homo sapiens	P01857 (AlphaFold model)
MB007 IgG1 Fab fragment light chain	L	protein	216	Homo sapiens	P0DOY2 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>4EOW_1 MB007 human IgG1 Fab fragment heavy chain (chains H)
QVHLVQSGSELKKPGASVKVSCKASGYSFSRYGIKWVRQAPGQGLEWMGWINTRSGVPAY
AQGFTGRFVFSLDTSVDTAFLEISSLKTEDTGIYYCATRPPRFYDKTEYWEDGFDVWGRG
TLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK

Sequence of entity 2 (L), FASTA

>4EOW_2 MB007 IgG1 Fab fragment light chain (chains L)
QSVLTQPPSASGTPGQSVNISCSGSSSNIGNSYVYWYQQLPGTAPKLLIYRNNRRPSGVP
DRFSGSKSDTSASLAISGLRSEDEADYYCATWDDSLSGRLFGGGTKLTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Primary citation

Molecular structure of human GM-CSF in complex with a disease-associated anti-human GM-CSF autoantibody and its potential biological implications. Blech, M., Seeliger, D., Kistler, B. et al. Biochem J (2012) 447:205-215. DOI 10.1042/BJ20120884 · PubMed

Other PDB entries of the same protein (UniProt P01857 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4LLD 1.19 Å, Structure of wild-type IgG1 antibody heavy chain constant domain 1 and light chain…
3TV3 1.29 Å, Crystal structure of broad and potent HIV-1 neutralizing antibody PGT128 in complex with…
4LLQ 1.42 Å, Structure of redesigned IgG1 first constant and lambda domains (CH1:Clambda constant…
5HSF 1.52 Å, 1.52 Angstrom Crystal Structure of Fc fragment of Human IgG1.
6YT7 1.55 Å, Glycosylated knob/dummy-hole fc fragment
4NWU 1.6 Å, Crystal structure of APE1551, an anti-human NGF Fab with a nine amino acid insertion in…
1L6X 1.65 Å, Fc fragment of rituximab bound to a minimized version of the B-domain from protein A…
3TWC 1.65 Å, Crystal structure of broad and potent HIV-1 neutralizing antibody PGT127 in complex with…
5JIH 1.66 Å, Crystal structure of HER2 binding IgG1-Fc (Fcab STAB19)
3MCL 1.7 Å, Anti-beta-amyloid antibody c706 fab in space group P21
5U66 1.7 Å, Modified single helix from the B-domain of protein A bound to IgG1 Fc
6N35 1.75 Å, Anti-HIV-1 Fab 2G12 + Man1-2 re-refinement

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