8DA3: Coevolved affibody-Z domain pair LL1.c1

Coevolved affibody-Z domain pair LL1.c1. Determined by X-ray diffraction at 1.06 Å resolution. Released 26 Jul 2023.

Method: X-ray diffraction
Resolution: 1.06 Å
Organisms: Staphylococcus aureus, synthetic construct
Chains: 2
Atoms: 1,160
Mol. weight: 15.99 kDa
Ligands: MLI
Released: 26 Jul 2023

Explore 8DA3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DA3 contains 9 α-helices and 0 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: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	3-5	3
α-helix	7-18	12
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	7-18	12
α-helix	24-36	13
α-helix	38-40	3
α-helix	41-54	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin G-binding protein A	A	protein	67	Staphylococcus aureus	P02976 (AlphaFold model)
Affibody LL1.FILF	B	protein	67	synthetic construct

Sequence of entity 1 (A), FASTA

>8DA3_1 Immunoglobulin G-binding protein A (chains A)
AVDNKFNKELQNAIYEIFHLPNLNEEQRNAFFQSLKDDPSQSANLLAEAKKLNDAQAPKL
EHHHHHH

Sequence of entity 2 (B), FASTA

>8DA3_2 Affibody LL1.FILF (chains B)
AVDNKFNKEFSVAGREIITLPNLNDPQKKAFLFSLWDDPSQSANLLAEAKKLNDAQAPKL
EHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
MLI	Malonate ion	C3 H2 O4	2

Water and common crystallization additives (SO4) are not listed.

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
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
5U3D 1.77 Å, Structure of meditope enabled trastuzumab I83E variant

Browse structure collections

About this viewer

MolViewer shows 8DA3 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.