1DQJ: Anti-lysozyme antibody hyhel-63

Crystal structure of the anti-lysozyme antibody hyhel-63 complexed with hen egg white lysozyme. Determined by X-ray diffraction at 2.0 Å resolution. Released 19 Jan 2000.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Mus musculus, Gallus gallus
Chains: 3
Atoms: 4,793
Mol. weight: 60.47 kDa
Released: 19 Jan 2000

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

Secondary structure: helices and β-sheets

1DQJ contains 21 α-helices and 55 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, 23 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	45-49	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	4
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	153-155	3	6
β-strand	159-163	5	5
α-helix	164-165	2
α-helix	167	1
β-strand	173-182	10	5
α-helix	183-188	6
β-strand	191-197	7	6
α-helix	204	1
β-strand	205-210	6	6

Chain B: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
β-strand	18-25	8	7
β-strand	34-39	6	9
β-strand	45-51	7	9
β-strand	57-59	3	9
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	87-89	3
β-strand	91-97	7	9
β-strand	103	1	9
β-strand	107-109	3	9
β-strand	110-111	2	8
β-strand	117	1	10
α-helix	118-119	2
β-strand	120-124	5	11
β-strand	135-145	11	11
β-strand	146	1	10
β-strand	151-155	4	12
α-helix	160-162	3
β-strand	164	1	12
β-strand	169-171	3	11
α-helix	172-174	3
β-strand	175-177	3	11
β-strand	182-192	11	11
β-strand	204-210	6	12
α-helix	211-213	3
β-strand	215-220	6	12

Chain C: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	13
α-helix	5-14	10
β-strand	20	1	14
β-strand	23	1	14
α-helix	25-36	12
β-strand	39	1	13
β-strand	43-45	3	15
β-strand	51-53	3	15
β-strand	58-59	2	15
β-strand	65	1	16
β-strand	79	1	16
α-helix	80-83	4
α-helix	89-98	10
α-helix	104-107	4
α-helix	109-114	6
α-helix	120-123	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Anti-lysozyme antibody hyhel-63 (light chain)	A	protein	214	Mus musculus	P01837 (AlphaFold model)
Anti-lysozyme antibody hyhel-63 (heavy chain)	B	protein	210	Mus musculus	P01865 (AlphaFold model)
Lysozyme	C	protein	129	Gallus gallus	P00698 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1DQJ_1 ANTI-LYSOZYME ANTIBODY HYHEL-63 (LIGHT CHAIN) (chains A)
DIVLTQSPATLSVTPGDSVSLSCRASQSISNNLHWYQQKSHESPRLLIKYASQSISGIPS
RFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSWPYTFGGGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (B), FASTA

>1DQJ_2 ANTI-LYSOZYME ANTIBODY HYHEL-63 (HEAVY CHAIN) (chains B)
EVQLQESGPSLVKPSQTLSLTCSVTGDSVTSDYWSWIRKFPGNKLEYMGYISYSGSTYYH
PSLKSRISITRDTSKNQYYLQLNSVTTEDTATYYCASWGGDVWGAGTTVTVSSAKTTAPS
VYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSS
VTVTSSTWPSQSITCNVAHPASSTKVDKKI

Sequence of entity 3 (C), FASTA

>1DQJ_3 LYSOZYME (chains C)
KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINS
RWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDV
QAWIRGCRL

Primary citation

Three-dimensional structures of the free and antigen-bound Fab from monoclonal antilysozyme antibody HyHEL-63(,). Li, Y., Li, H., Smith-Gill, S.J. et al. Biochemistry (2000) 39:6296-6309. DOI 10.1021/bi000054l · 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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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…

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