3D9A: Lysozyme C

High Resolution Crystal Structure Structure of HyHel10 Fab Complexed to Hen Egg Lysozyme. Determined by X-ray diffraction at 1.2 Å resolution. Released 10 Jun 2008.

Method: X-ray diffraction
Resolution: 1.2 Å
Organisms: Gallus gallus, Mus musculus
Chains: 3
Atoms: 4,947
Mol. weight: 60.57 kDa
Released: 10 Jun 2008

Explore 3D9A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3D9A contains 25 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 C: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	602	1	1
α-helix	605-614	10
β-strand	620	1	2
β-strand	623	1	2
α-helix	625-636	12
β-strand	639	1	1
β-strand	643-645	3	3
β-strand	651-653	3	3
β-strand	658-659	2	3
β-strand	665	1	4
β-strand	679	1	4
α-helix	680-684	5
α-helix	689-699	11
α-helix	704-707	4
α-helix	709-714	6
α-helix	720-724	5

Chain H: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	303-307	5	10
β-strand	311-312	2	11
β-strand	318-325	8	10
α-helix	329-331	3
β-strand	334-340	7	12
β-strand	344-351	8	12
β-strand	357-359	3	12
α-helix	361-363	3
β-strand	367-372	6	10
α-helix	373-375	3
β-strand	377-382	6	10
α-helix	387-389	3
β-strand	391-397	7	12
β-strand	403	1	12
β-strand	407-409	3	12
β-strand	410-411	2	11
α-helix	414-416	3
β-strand	417	1	13
α-helix	418-419	2
β-strand	420-424	5	14
β-strand	435-445	11	14
β-strand	446	1	13
β-strand	451-454	4	15
α-helix	455-457	3
β-strand	459	1	15
β-strand	463-465	3	14
α-helix	466-468	3
β-strand	469-471	3	14
β-strand	474-484	11	14
α-helix	485-487	3
β-strand	494-499	6	15
α-helix	500-502	3
β-strand	504-509	6	15

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	5
β-strand	10-13	4	6
β-strand	19-25	7	5
β-strand	33-38	6	6
β-strand	45-49	5	6
β-strand	53-54	2	6
β-strand	62-67	6	5
β-strand	70-75	6	5
α-helix	80-82	3
β-strand	84-90	7	6
α-helix	96	1
β-strand	97-98	2	6
β-strand	102-106	5	6
β-strand	111	1	7
α-helix	112-113	2
β-strand	114-118	5	8
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	8
β-strand	140	1	7
β-strand	145-150	6	9
β-strand	153-155	3	9
β-strand	159-163	5	8
α-helix	164-167	4
β-strand	173-182	10	8
α-helix	183-188	6
β-strand	191-197	7	9
α-helix	204	1
β-strand	205-210	6	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysozyme C	C	protein	129	Gallus gallus	P00698 (AlphaFold model)
Light Chain of HyHel10 Antibody Fragment (Fab)	L	protein	213	Mus musculus	P01837 (AlphaFold model)
Heavy Chain of HyHel10 Antibody Fragment (Fab)	H	protein	210	Mus musculus

Sequence of entity 1 (C), FASTA

>3D9A_1 Lysozyme C (chains C)
KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINS
RWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDV
QAWIRGCRL

Sequence of entity 2 (L), FASTA

>3D9A_2 Light Chain of HyHel10 Antibody Fragment (Fab) (chains L)
DIVLTQSPATLSVTPGNSVSLSCRASQSIGNNLHWYQQKSHESPRLLIKYASQSISGIPS
RFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSWPYTFGGGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE

Sequence of entity 3 (H), FASTA

>3D9A_3 Heavy Chain of HyHel10 Antibody Fragment (Fab) (chains H)
DVQLQESGPSLVKPSQTLSLTCSVTGDSITSDYWSWIRKFPGNRLEYMGYVSYSGSTYYN
PSLKSRISITRDTSKNQYYLDLNSVTTEDTATYYCANWDGDYWGQGTLVTVSAAKTTPPS
VYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSS
VTVPSSTWPSETVTCNVAHPASSTKVDKKI

Primary citation

Light chain somatic mutations change thermodynamics of binding and water coordination in the HyHEL-10 family of antibodies. Acchione, M., Lipschultz, C.A., DeSantis, M.E. et al. Mol Immunol (2009) 47:457-464. DOI 10.1016/j.molimm.2009.08.018 · PubMed

Other PDB entries of the same protein (UniProt P00698 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2VB1 0.65 Å, HEWL at 0.65 angstrom resolution
8ZST 0.8 Å, Lysozyme Crystallized with Bioassembler on Earth
9QUM 0.83 Å, Structure of lysozyme by continuous serial electron diffraction (SerialED)
7SKW 0.87 Å, Ab initio structure of triclinic lysozyme from electron-counted MicroED data
7ULY 0.87 Å, MicroED structure of triclinic lysozyme
7P6M 0.89 Å, Hydrogenated refolded hen egg-white lysozyme
9RZL 0.9 Å, Hen egg-white lysozyme (HEWL)
8RLI 0.91 Å, Neutron structure of perdeuterated hen egg-white lysozyme at room temperature
7YRK 0.92 Å, Crystal structure of the hen egg lysozyme-2-oxidobenzylidene-threoninato-copper (II)…
3LZT 0.93 Å, Refinement of triclinic lysozyme at atomic resolution
1IEE 0.94 Å, Structure of tetragonal hen egg white lysozyme at 0.94 a from crystals grown by the…
7OL5 0.94 Å, Crystal structure of Lysozyme in complex with Hepes

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