1NBY: HyHEL-63

Crystal Structure of HyHEL-63 complexed with HEL mutant K96A. Determined by X-ray diffraction at 1.8 Å resolution. Released 1 Apr 2003.

Method: X-ray diffraction
Resolution: 1.8 Å
Organisms: Mus musculus, Gallus gallus
Chains: 3
Atoms: 4,911
Mol. weight: 60.41 kDa
Released: 1 Apr 2003

Explore 1NBY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1NBY contains 23 α-helices and 56 β-strands across 3 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: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	15	1	3
β-strand	17	1	3
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	45-48	4	2
β-strand	49	1	4
β-strand	53	1	4
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	5
β-strand	114-118	5	6
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	6
β-strand	140	1	5
β-strand	145-150	6	7
β-strand	153-155	3	7
β-strand	159-163	5	6
α-helix	164-165	2
α-helix	167	1
β-strand	173-182	10	6
α-helix	183-186	4
β-strand	191-197	7	7
α-helix	204	1
β-strand	205-210	6	7

Chain B: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	303-307	5	8
β-strand	311-312	2	9
β-strand	318-325	8	8
α-helix	329-331	3
β-strand	334-340	7	2
β-strand	344-351	8	2
β-strand	357-359	3	2
β-strand	367-372	6	8
β-strand	377-382	6	8
α-helix	387-389	3
β-strand	391-397	7	2
β-strand	403	1	2
β-strand	407-409	3	2
β-strand	410-411	2	9
α-helix	414-416	3
β-strand	417	1	10
α-helix	418-419	2
β-strand	420-424	5	11
α-helix	427-429	3
β-strand	435-445	11	11
β-strand	446	1	10
β-strand	451-454	4	12
α-helix	455-457	3
β-strand	459	1	12
β-strand	463-465	3	11
α-helix	466-468	3
β-strand	469-471	3	11
β-strand	474-484	11	11
β-strand	494-499	6	12
α-helix	500-502	3
β-strand	504-509	6	12

Chain C: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	602	1	13
α-helix	605-614	10
β-strand	620	1	14
β-strand	623	1	14
α-helix	625-636	12
β-strand	639	1	13
β-strand	643-645	3	15
β-strand	651-653	3	15
β-strand	658-659	2	15
β-strand	665	1	16
β-strand	679	1	16
α-helix	680-684	5
α-helix	689-698	10
α-helix	704-707	4
α-helix	709-714	6
α-helix	720-723	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
antibody kappa light chain	A	protein	214	Mus musculus	P01837 (AlphaFold model)
immunoglobulin gamma 1 chain	B	protein	210	Mus musculus	P01865 (AlphaFold model)
Lysozyme C	C	protein	129	Gallus gallus	P00698 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1NBY_1 antibody kappa light chain (chains A)
DIVLTQSPATLSVTPGDSVSLSCRASQSISNNLHWYQQKSHESPRLLIKYASQSISGIPS
RFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSWPYTFGGGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (B), FASTA

>1NBY_2 immunoglobulin gamma 1 chain (chains B)
EVQLQESGPSLVKPSQTLSLTCSVTGDSVTSDYWSWIRKFPGNKLEYMGYISYSGSTYYH
PSLKSRISITRDTSKNQYYLQLNSVTTEDTATYYCASWGGDVWGAGTTVTVSSAKTTAPS
VYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSS
VTVTSSTWPSQSITCNVAHPASSTKVDKKI

Sequence of entity 3 (C), FASTA

>1NBY_3 Lysozyme C (chains C)
KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINS
RWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAAKIVSDGNGMNAWVAWRNRCKGTDV
QAWIRGCRL

Primary citation

Dissection of binding interactions in the complex between the anti-lysozyme antibody HyHEL-63 and its antigen. Li, Y., Urrutia, M., Smith-Gill, S.J. et al. Biochemistry (2003) 42:11-22. DOI 10.1021/bi020589+ · PubMed

Other PDB entries of the same protein (UniProt P01837 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3D9A 1.2 Å, High Resolution Crystal Structure Structure of HyHel10 Fab Complexed to Hen Egg Lysozyme
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2W9D 1.57 Å, Structure of Fab fragment of the ICSM 18 - anti-Prp therapeutic antibody at 1.57 A…
3BKJ 1.59 Å, Crystal structure of Fab wo2 bound to the n terminal domain of amyloid beta peptide (1-16)
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2R1Y 1.6 Å, Crystal structure of S25-2 Fab in complex with Kdo analogues
2R2B 1.6 Å, Crystal structure of S25-2 Fab in complex with Kdo analogues
3BKM 1.6 Å, Structure of anti-amyloid-beta Fab WO2 (Form A, P212121)
3CFB 1.6 Å, High-resolution structure of blue fluorescent antibody EP2-19G2 in complex with stilbene…

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