6K3M: SpA IgG-binding domain protein,Protein A

Application of anti-helix antibodies in protein structure determination (8189-3LRH). Determined by X-ray diffraction at 1.8 Å resolution. Released 14 Aug 2019.

Method: X-ray diffraction
Resolution: 1.8 Å
Organisms: Staphylococcus aureus, Homo sapiens
Chains: 2
Atoms: 1,449
Mol. weight: 23.51 kDa
Released: 14 Aug 2019

Explore 6K3M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6K3M contains 6 α-helices and 11 β-strands across 2 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: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	1
β-strand	9-12	4	2
β-strand	18-23	6	1
β-strand	35-39	5	2
β-strand	46-50	5	2
β-strand	54-55	2	2
α-helix	56	1
β-strand	63-68	6	1
β-strand	71-76	6	1
α-helix	81-83	3
β-strand	85-93	9	2
β-strand	98-101	4	2
β-strand	105-109	5	2

Chain H: 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	39-62	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SpA IgG-binding domain protein,Protein A	H	protein	82	Staphylococcus aureus	P02976 (AlphaFold model)
3LRH intrabody	A	protein	135	Homo sapiens

Sequence of entity 1 (H), FASTA

>6K3M_1 SpA IgG-binding domain protein,Protein A (chains H)
MGSSHHHHHHSSGLVPRGSHMFNKDQQSAFYEILNMPNLNEAQRNGFIQSLKDDPSQSTN
VLGEAKKLNKLQKAFESLKSFQ

Sequence of entity 2 (A), FASTA

>6K3M_2 3LRH intrabody (chains A)
MGSSHHHHHHSSGLVPRGSHMGSQPVLTQSPSVSAAPRQRVTISVSGSNSNIGSNTVNWI
QQLPGRAPELLMYDDDLLAPGVSDRFSGSRSGTSASLTISGLQSEDEADYYAATWDDSLN
GWVFGGGTKVTVLSA

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
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

Browse structure collections

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