2DD8: SARS-CoV Spike Receptor-Binding Domain

Crystal Structure of SARS-CoV Spike Receptor-Binding Domain Complexed with Neutralizing Antibody. Determined by X-ray diffraction at 2.3 Å resolution. Released 4 Apr 2006.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Homo sapiens, SARS coronavirus
Chains: 3
Atoms: 5,057
Mol. weight: 71.86 kDa
Ligands: NAG, PO4
Released: 4 Apr 2006

Explore 2DD8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2DD8 contains 26 α-helices and 63 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 H: 11 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-24	7	1
β-strand	34-39	6	2
β-strand	46-52	7	2
α-helix	52A-54	3
β-strand	56-59	4	2
α-helix	61-63	3
β-strand	67-71	5	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-95	8	2
α-helix	96	1
β-strand	100A-103	4	2
β-strand	107-111	5	2
α-helix	115-116	2
β-strand	117	1	3
β-strand	120-124	5	4
α-helix	125-127	3
β-strand	135-145	11	4
β-strand	146	1	3
β-strand	151-154	4	5
α-helix	155-157	3
β-strand	159	1	5
β-strand	163-165	3	4
α-helix	166-168	3
β-strand	169-170	2	4
β-strand	176-185	10	4
α-helix	186-190	5
β-strand	195-200	6	5
α-helix	201-203	3
β-strand	205-210	6	5

Chain L: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	6
β-strand	10-13	4	7
β-strand	19-24	6	6
α-helix	28-30	3
β-strand	34-38	5	7
β-strand	45-48	4	7
β-strand	49	1	8
β-strand	53	1	8
α-helix	54-55	2
β-strand	62-67	6	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	84-92	9	7
β-strand	95A-98	4	7
β-strand	102-106	5	7
α-helix	109-111	3
β-strand	112	1	9
β-strand	115-119	5	10
α-helix	120-122	3
α-helix	123-126	4
β-strand	131-140	10	10
β-strand	141	1	9
β-strand	146-151	6	11
β-strand	154-155	2	11
β-strand	160-162	3	10
α-helix	163-165	3
β-strand	166-167	2	10
β-strand	174-182	9	10
α-helix	184-189	6
β-strand	193-199	7	11
β-strand	202-208	7	11

Chain S: 7 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	322	1	12
α-helix	326-329	4
β-strand	336	1	13
β-strand	341-345	5	13
β-strand	348-349	2	12
α-helix	353-356	4
β-strand	363-367	5	13
α-helix	371-373	3
β-strand	378-379	2	12
β-strand	381-390	10	13
α-helix	391-396	6
α-helix	404-408	5
β-strand	418-424	7	13
α-helix	426-429	4
β-strand	431	1	14
β-strand	435	1	15
β-strand	439-441	3	16
β-strand	460	1	17
β-strand	475	1	17
β-strand	478-480	3	16
β-strand	483	1	15
β-strand	484	1	14
α-helix	489-491	3
β-strand	493-502	10	13
β-strand	510-511	2	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
IGG Heavy Chain	H	protein	245	Homo sapiens	Q6PJF1
IGG Light Chain	L	protein	213	Homo sapiens	Q8N355 (AlphaFold model)
Spike glycoprotein	S	protein	202	SARS coronavirus	P59594

Sequence of entity 1 (H), FASTA

>2DD8_1 IGG Heavy Chain (chains H)
QVQLQQSGAEVKKPGSSVKVSCKASGGTFSSYTISWVRQAPGQGLEWMGGITPILGIANY
AQKFQGRVTITTDESTSTAYMELSSLRSEDTAVYYCARDTVMGGMDVWGQGTTVTVSSAS
TKGPSVFPLAPSSKSTSGGTSALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTSPLFVHHHHHHGDYKD
DDDKG

Sequence of entity 2 (L), FASTA

>2DD8_2 IGG Light Chain (chains L)
SYELTQPPSVSVAPGKTARITCGGNNIGSKSVHWYQQKPGQAPVLVVYDDSDRPSGIPER
FSGSNSGNTATLTISRVEAGDEADYYCQVWDSSSDYVFGTGTKVTVLGQPKANPTVTLFP
PSSEEFQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLS
LTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 3 (S), FASTA

>2DD8_3 Spike glycoprotein (chains S)
PNITNLCPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLND
LCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNY
NYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRV
VVLSFELLNAPATVCGPKLSTD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
PO4	Phosphate ion	O4 P	1

Primary citation

Structure of Severe Acute Respiratory Syndrome Coronavirus Receptor-binding Domain Complexed with Neutralizing Antibody. Prabakaran, P., Gan, J., Feng, Y. et al. J Biol Chem (2006) 281:15829-15836. DOI 10.1074/jbc.M600697200 · PubMed

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