4NWT: Anti-human NGF Fab APE1531

Crystal structure of the anti-human NGF Fab APE1531. Determined by X-ray diffraction at 1.75 Å resolution. Released 22 Oct 2014.

Method: X-ray diffraction
Resolution: 1.75 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,982
Mol. weight: 50.07 kDa
Released: 22 Oct 2014

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

Secondary structure: helices and β-sheets

4NWT contains 13 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: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
β-strand	10-12	3	2
β-strand	18-25	8	7
β-strand	33-39	7	2
β-strand	45-52	8	2
β-strand	56-59	4	2
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-95	8	2
β-strand	97-100	4	8
β-strand	100E-100H	4	8
β-strand	102-103	2	2
β-strand	107-111	5	2
α-helix	115-116	2
β-strand	117	1	9
β-strand	120-124	5	10
β-strand	133-134	2	10
β-strand	137-147	11	10
β-strand	148	1	9
β-strand	153-157	4	11
α-helix	162-164	3
β-strand	166	1	11
β-strand	171-173	3	10
α-helix	174-176	3
β-strand	177-178	2	10
β-strand	185-194	10	10
α-helix	195-197	3
β-strand	207-212	6	11
α-helix	213-215	3
β-strand	217-222	6	11

Chain L: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	19-25	7	1
β-strand	27C-27D	2	3
β-strand	30-31	2	3
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
β-strand	97-98	2	2
β-strand	102-107	6	2
β-strand	111	1	4
α-helix	112-113	2
β-strand	114-118	5	5
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	5
β-strand	140	1	4
β-strand	145-150	6	6
β-strand	153-154	2	6
β-strand	159-163	5	5
α-helix	164-167	4
β-strand	173-182	10	5
α-helix	183-187	5
β-strand	191-197	7	6
β-strand	205-210	6	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
APE1531 Ab Fab light chain	L	protein	220	Homo sapiens	Q8TCD0 (AlphaFold model)
APE1531 Ab Fab heavy chain	H	protein	233	Homo sapiens	P01857 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>4NWT_1 APE1531 Ab Fab light chain (chains L)
DIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNKNYLTWYQQKPGQPPKLLIYWASTR
ESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYDNYPITFGQGTRLEIKRTVAAPS
VFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYS
LSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (H), FASTA

>4NWT_2 APE1531 Ab Fab heavy chain (chains H)
QVQLVQSGAEVKKPGSSVKVSCKASGGTFSNYAISWVRQAPGQGFEWMGGIIPIFGTANY
AQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARGPEYYDYVWGSYRYNYFDYWGQ
GTLVTVSSGSASAPTLFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

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 Q8TCD0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4NWU 1.6 Å, Crystal structure of APE1551, an anti-human NGF Fab with a nine amino acid insertion in…
6ARP 1.7 Å, Structure of a mutant Cetuximab Fab fragment
6DC4 1.7 Å, RSV-neutralizing human antibody AM22
6UC5 1.75 Å, Fab397 in complex with NPNA peptide
3MNZ 1.8 Å, Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment with a gp41…
4NUJ 1.83 Å, Crystal structure of HIV-1 broadly neutralizing antibody PGT152
4NUG 1.86 Å, Crystal structure of HIV-1 broadly neutralizing antibody PGT151
5VKK 2.01 Å, Crystal structure of Fab fragment of anti-CD22 Epratuzumab
3PGF 2.1 Å, Crystal structure of maltose bound MBP with a conformationally specific synthetic…
3MNW 2.2 Å, Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment with a gp41…
6E4X 2.25 Å, Human antibody S5V2-29 in complex with influenza hemagglutinin A/Texas/50/2012 (H3N2)
4D9Q 2.28 Å, Inhibiting Alternative Pathway Complement Activation by Targeting the Exosite on Factor D

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