6K65: Immunoglobulin G-binding protein A

Application of anti-helix antibodies in protein structure determination (9014-1P4B). Determined by X-ray diffraction at 1.65 Å resolution. Released 14 Aug 2019.

Method: X-ray diffraction
Resolution: 1.65 Å
Organisms: Staphylococcus aureus (strain NCTC 8325), Mus musculus
Chains: 3
Atoms: 2,441
Mol. weight: 32.94 kDa
Released: 14 Aug 2019

Explore 6K65 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6K65 contains 9 α-helices and 21 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: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	5-16	12
α-helix	22-34	13
α-helix	36-38	3
α-helix	39-60	22

Chain H: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	3
β-strand	17-25	9	3
β-strand	34-39	6	4
β-strand	45-51	7	4
β-strand	57-59	3	4
α-helix	64-66	3
β-strand	67-72	6	3
β-strand	77-82	6	3
α-helix	87-89	3
β-strand	91-97	7	4
β-strand	103	1	4
β-strand	107-109	3	4

Chain L: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	9-11	3	1
β-strand	14-17	4	2
β-strand	22-29	8	1
α-helix	36-38	3
β-strand	41-46	6	2
β-strand	50-56	7	2
β-strand	60-61	2	2
α-helix	62	1
β-strand	69-74	6	1
β-strand	77-83	7	1
α-helix	87-89	3
β-strand	91-99	9	2
β-strand	102-105	4	2
β-strand	109-113	5	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin G-binding protein A	A	protein	78	Staphylococcus aureus (strain NCTC 8325)	P02976 (AlphaFold model)
1P4B variable light chain	L	protein	115	Mus musculus
1P4B variable heavy chain	H	protein	113	Mus musculus

Sequence of entity 1 (A), FASTA

>6K65_1 Immunoglobulin G-binding protein A (chains A)
MGSSHHHHHHSSGLVPRGSHMKEQQNAFYEILHLPNLNEEQRNAFIQSLKDDPSQSANLL
AEAKALNHLQNEVARLKK

Sequence of entity 2 (L), FASTA

>6K65_2 1P4B variable light chain (chains L)
DAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYASWVQEKPDHLFTGLIGGTNNRAPGV
PARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVLGGGGGS

Sequence of entity 3 (H), FASTA

>6K65_3 1P4B variable heavy chain (chains H)
DVQLQQSGPGLVAPSQSLSITCTVSGFSLTDYGVNWVRQSPGKGLEWLGVIWGDGITDYN
SALKSRLSVTKDNSKSQVFLKMNSLQSGDSARYYCVTGLFDYWGQGTTLTVSS

Primary citation

Application of antihelix antibodies in protein structure determination. Kim, J.W., Kim, S., Lee, H. et al. Proc Natl Acad Sci U S A (2019) 116:17786-17791. DOI 10.1073/pnas.1910080116 · 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
9M6O 1.49 Å, Crystal structure of S. aureus protein A bound to a camelid single-domain antibody
8DA6 1.5 Å, Coevolved affibody-Z domain pair LL1.c5
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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