8DA4: Coevolved affibody-Z domain pair LL1.c2

Coevolved affibody-Z domain pair LL1.c2. Determined by X-ray diffraction at 1.92 Å resolution. Released 26 Jul 2023.

Method: X-ray diffraction
Resolution: 1.92 Å
Organisms: Staphylococcus aureus, synthetic construct
Chains: 6
Atoms: 2,737
Mol. weight: 46.6 kDa
Released: 26 Jul 2023

Explore 8DA4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DA4 contains 24 α-helices and 0 β-strands across 6 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 C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	4-18	15
α-helix	24-36	13
α-helix	38-40	3
α-helix	41-54	14

Chain B: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	7-16	10
α-helix	24-36	13
α-helix	38-40	3
α-helix	41-54	14

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	8-17	10
α-helix	24-36	13
α-helix	38-40	3
α-helix	41-54	14

Chain E: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	5-18	14
α-helix	24-36	13
α-helix	38-40	3
α-helix	41-55	15

Chain F: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	7-17	11
α-helix	24-36	13
α-helix	38-40	3
α-helix	41-55	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin G-binding protein A	A, C, E	protein	67	Staphylococcus aureus	P02976 (AlphaFold model)
Affibody LL1.FIVM	B	protein	67	synthetic construct
affibody LL1.FIVM	D, F	protein	67	synthetic construct

Sequence of entity 1 (A, C, E), FASTA

>8DA4_1 Immunoglobulin G-binding protein A (chains A, C, E)
AVDNKFNKELQNAIYEILHLPNLNEEQRNAFFQSLKDDPSQSANLLAEAKKLNDAQAPKL
EHHHHHH

Sequence of entity 2 (B), FASTA

>8DA4_2 Affibody LL1.FIVM (chains B)
AVDNKFNKEFSVAGREIITLPNLNDPQKKAFVMSLWDDPSQSANLLAEAKKLNDAQAPKL
EHHHHHH

Sequence of entity 3 (D, F), FASTA

>8DA4_3 affibody LL1.FIVM (chains D, F)
AVDNKFNKEFSVAGREIITLPNLNDPQKKAFVMSLWDDPSQSANLLAEAKKLNDAQAPKL
EHHHHHH

Primary citation

Deploying synthetic coevolution and machine learning to engineer protein-protein interactions. Yang, A., Jude, K.M., Lai, B. et al. Science (2023) 381:eadh1720-eadh1720. DOI 10.1126/science.adh1720 · 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

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