1NDG: Fab fragment of antibody HyHEL-8

Crystal structure of Fab fragment of antibody HyHEL-8 complexed with its antigen lysozyme. Determined by X-ray diffraction at 1.9 Å resolution. Released 3 Jun 2003.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Mus musculus, Gallus gallus
Chains: 3
Atoms: 4,781
Mol. weight: 60.62 kDa
Released: 3 Jun 2003

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

Secondary structure: helices and β-sheets

1NDG contains 23 α-helices and 53 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: 9 helices, 21 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
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	153-155	3	5
β-strand	159-163	5	4
α-helix	164-165	2
α-helix	167	1
β-strand	173-182	10	4
α-helix	183-186	4
β-strand	191-197	7	5
α-helix	204	1
β-strand	205-210	6	5

Chain B: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	303-307	5	6
β-strand	311-312	2	7
β-strand	318-325	8	6
α-helix	329-331	3
β-strand	334-340	7	8
β-strand	344-351	8	8
β-strand	357-359	3	8
α-helix	361-363	3
β-strand	367-372	6	6
β-strand	377-382	6	6
α-helix	387-389	3
β-strand	391-397	7	8
β-strand	403	1	8
β-strand	407-409	3	8
β-strand	410-411	2	7
β-strand	417	1	9
α-helix	418-419	2
β-strand	420-424	5	10
β-strand	435-445	11	10
β-strand	446	1	9
β-strand	451-455	4	11
α-helix	460-462	3
β-strand	464	1	11
β-strand	469-471	3	10
α-helix	472-474	3
β-strand	475-477	3	10
β-strand	482-492	11	10
β-strand	506-510	5	11
α-helix	511-513	3
β-strand	515-519	5	11

Chain C: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	602	1	12
α-helix	605-614	10
β-strand	620	1	13
β-strand	623	1	13
α-helix	625-636	12
β-strand	639	1	12
β-strand	643-645	3	14
β-strand	651-653	3	14
β-strand	658-659	2	14
β-strand	665	1	15
β-strand	679	1	15
α-helix	680-684	5
α-helix	689-699	11
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

>1NDG_1 antibody kappa light chain (chains A)
DIVLTQSPATLSVTPGDSVSLSCRASQSISNNLHWYQQKSHESPRLLIKYASQSISGIPS
RFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSWPYTFGGGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (B), FASTA

>1NDG_2 immunoglobulin gamma 1 chain (chains B)
EVQLQESGPSLVKPSQTLSLTCSVTGDSIIRDYWSWIRKFPGNKLEYMGYISFSGNTFYH
PSLKSRISITRDTSKNQHYLQLSSVTTEDTATYYCANWDGTYWGEGTLVTVSAAKTTAPS
VYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSS
VTVTSSTWPSQSITCNVAHPASSTAVDKKI

Sequence of entity 3 (C), FASTA

>1NDG_3 Lysozyme C (chains C)
KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINS
AWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDV
QAWIRGCRL

Primary citation

X-ray snapshots of the maturation of an antibody response to a protein antigen. Li, Y., Li, H., Yang, F. et al. Nat Struct Biol (2003) 10:482-488. DOI 10.1038/nsb930 · 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
1RUR 1.5 Å, Crystal Structure (I) of native Diels-Alder antibody 13G5 Fab at pH 8.0 with a data set…
2AJU 1.5 Å, Cyrstal structure of cocaine catalytic antibody 7A1 Fab'
2AJV 1.5 Å, Crystal Structure of Cocaine catalytic Antibody 7A1 Fab' in Complex with Cocaine
2W60 1.5 Å, Anti citrullinated Collagen type 2 antibody acc4
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)
3BAE 1.59 Å, Crystal structure of Fab WO2 bound to the N terminal domain of Amyloid beta peptide (1-28)
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…

Browse structure collections

About this viewer

MolViewer shows 1NDG directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.