4NWU: APE1551 Ab Fab heavy chain

Crystal structure of APE1551, an anti-human NGF Fab with a nine amino acid insertion in CDR H1. Determined by X-ray diffraction at 1.6 Å resolution. Released 22 Oct 2014.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,178
Mol. weight: 50.31 kDa
Released: 22 Oct 2014

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

Secondary structure: helices and β-sheets

4NWU contains 19 α-helices and 48 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: 10 helices, 25 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
α-helix	33C-33G	5
β-strand	33I-39	7	2
β-strand	45-52	8	2
β-strand	56-59	4	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	88-95	8	2
β-strand	97-100	4	3
β-strand	100E-100H	4	3
β-strand	102-103	2	2
β-strand	107-111	5	2
α-helix	115-116	2
β-strand	117	1	4
α-helix	118-119	2
β-strand	120-124	5	5
β-strand	133-134	2	5
β-strand	137-147	11	5
β-strand	148	1	4
β-strand	153-157	4	6
α-helix	162-164	3
β-strand	166	1	6
β-strand	171-173	3	5
α-helix	174-176	3
β-strand	177-178	2	5
β-strand	185-194	10	5
α-helix	195-197	3
β-strand	206-212	7	6
α-helix	213-215	3
β-strand	217-225	7	6

Chain L: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-14	5	8
β-strand	19-25	7	7
β-strand	27C-27D	2	9
β-strand	30-31	2	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	102-107	6	8
β-strand	111	1	10
α-helix	112-113	2
β-strand	114-118	5	11
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	11
β-strand	140	1	10
β-strand	145-150	6	12
β-strand	153-154	2	12
α-helix	155	1
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
APE1551 Ab Fab heavy chain	H	protein	242	Homo sapiens	P01857 (AlphaFold model)
APE1551 Ab Fab light chain	L	protein	220	Homo sapiens	Q8TCD0 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>4NWU_1 APE1551 Ab Fab heavy chain (chains H)
QVQLVQSGAEVKKPGSSVKVSCKASGDTFSNYATGDTFSNYAISWVRQAPGQGFEWMGGI
IPIFGTANYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARGPEYYDYVWGSYR
YNYFDYWGQGTLVTVSSGSASAPTLFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNS
GALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC
DK

Sequence of entity 2 (L), FASTA

>4NWU_2 APE1551 Ab Fab light chain (chains L)
DIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNKNYLTWYQQKPGQPPKLLIYWASTR
ESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYDNYPITFGQGTRLEIKRTVAAPS
VFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYS
LSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

Nucleotide insertions and deletions complement point mutations to massively expand the diversity created by somatic hypermutation of antibodies. Bowers, P.M., Verdino, P., Wang, Z. et al. J Biol Chem (2014) 289:33557-33567. DOI 10.1074/jbc.M114.607176 · 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
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
3DJ9 1.75 Å, Crystal Structure of an isolated, unglycosylated antibody CH2 domain

Browse structure collections

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