9M6O: S. aureus protein A

Crystal structure of S. aureus protein A bound to a camelid single-domain antibody. Determined by X-ray diffraction at 1.49 Å resolution. Released 12 Nov 2025.

Method: X-ray diffraction
Resolution: 1.49 Å
Organisms: Staphylococcus aureus (strain NCTC 8325 / PS 47), Camelus dromedarius
Chains: 4
Atoms: 3,151
Mol. weight: 41.59 kDa
Released: 12 Nov 2025

Explore 9M6O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9M6O contains 14 α-helices and 26 β-strands across 4 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.

Chains A and H: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	2805-2815	11
α-helix	2822-2834	13
α-helix	2836-2838	3
α-helix	2839-2852	14

Chain B: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-13	3	2
β-strand	18-25	8	1
β-strand	36-42	7	3
β-strand	48-55	8	3
β-strand	61-63	3	3
α-helix	65-67	3
β-strand	68	1	1
β-strand	71-76	6	1
β-strand	81-86	6	1
α-helix	91-93	3
β-strand	95-102	8	3
α-helix	111-113	3
β-strand	116-117	2	3
β-strand	121-123	3	3
β-strand	124-126	3	2

Chain C: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	4
β-strand	11-13	3	5
β-strand	18-25	8	4
β-strand	36-42	7	6
β-strand	49-55	7	6
β-strand	61-63	3	6
α-helix	65-67	3
β-strand	68	1	4
β-strand	71-76	6	4
β-strand	81-86	6	4
α-helix	91-93	3
β-strand	95-102	8	6
α-helix	111-113	3
β-strand	116-117	2	6
β-strand	121-123	3	6
β-strand	124-126	3	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin G-binding protein A	A, H	protein	61	Staphylococcus aureus (strain NCTC 8325 / PS 47)	P02976 (AlphaFold model)
single-domain antibody	B, C	protein	127	Camelus dromedarius

Sequence of entity 1 (A, H), FASTA

>9M6O_1 Immunoglobulin G-binding protein A (chains A, H)
ADAQQNNFNKDQQSAFYEILNMPNLNEAQRNGFIQSLKDDPSQSTNVLGEAKKLNESQAP
K

Sequence of entity 2 (B, C), FASTA

>9M6O_2 single-domain antibody (chains B, C)
QVQLQDSGGGLVQAGGSLRLSCAVSGRTFSAHSVYTMGWFRQAPGKEREFVARIYWSSAN
TYYADSVKGRFTISRDNAKNTVDLQMNSLRPEDTAVYYCAARDGIPTSRTVGSYNYWGQG
TQVTVSS

Primary citation

A synergistic generative-ranking framework for tailored design of therapeutic single-domain antibodies. Kong, Y., Shi, J., Wu, F. et al. Cell Discov (2025) 11:85-85. DOI 10.1038/s41421-025-00843-8 · PubMed

Other PDB entries of the same protein (UniProt P02976 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8DA5 1.0 Å, Coevolved affibody-Z domain pair LL1.c4
8DA7 1.02 Å, Coevolved affibody-Z domain pair LL1.c6
8DA3 1.06 Å, Coevolved affibody-Z domain pair LL1.c1
8DAB 1.13 Å, Coevolved affibody-Z domain pair LL2.c17
8DAC 1.19 Å, Coevolved affibody-Z domain pair LL2.c22
8DA8 1.29 Å, Coevolved affibody-Z domain pair LL2.c1
8DA9 1.35 Å, Coevolved affibody-Z domain pair LL2.c3
8DA6 1.5 Å, Coevolved affibody-Z domain pair LL1.c5
6K65 1.65 Å, Application of anti-helix antibodies in protein structure determination (9014-1P4B)
5U6A 1.74 Å, Crystal structure of I83E meditope-enabled trastuzumab with azido-PEG3-meditope
8DAA 1.75 Å, Coevolved affibody-Z domain pair LL2.c7
5U3D 1.77 Å, Structure of meditope enabled trastuzumab I83E variant

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