6NL9: Immunoglobulin G-binding protein G

Crystal structure of de novo designed metal-controlled dimer of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (L12H, T16L, V29H, Y33H, N37L)-apo. Determined by X-ray diffraction at 1.7 Å resolution. Released 23 Jan 2019.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Streptococcus
Chains: 4
Atoms: 1,938
Mol. weight: 25.08 kDa
Ligands: MG
Released: 23 Jan 2019

Explore 6NL9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6NL9 contains 6 α-helices and 16 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.

Chain A: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
β-strand	13-19	7	1
α-helix	23-36	14
β-strand	42-46	5	1
β-strand	51-55	5	1

Chains B and C: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	2
β-strand	13-19	7	2
α-helix	23-37	15
β-strand	42-46	5	2
α-helix	47-49	3
β-strand	51-55	5	2

Chain D: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	2
β-strand	13-19	7	2
α-helix	23-37	15
β-strand	42-46	5	2
β-strand	51-55	5	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin G-binding protein G	A, B, C, D	protein	56	Streptococcus	P19909 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>6NL9_1 Immunoglobulin G-binding protein G (chains A, B, C, D)
MTYKLILNGKTHKGELTTEAVDAATAEKHFKQHANDLGVDGEWTYDDATKTFTVTE

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

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

Primary citation

Design of High-Affinity Metal-Controlled Protein Dimers. Maniaci, B., Lipper, C.H., Anipindi, D.L. et al. Biochemistry (2019) 58:2199-2207. DOI 10.1021/acs.biochem.9b00055 · PubMed

Other PDB entries of the same protein (UniProt P19909 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3FIL 0.88 Å, Structural and energetic determinants for hyperstable variants of GB1 obtained from…
2QMT 1.05 Å, Crystal Polymorphism of Protein GB1 Examined by Solid-state NMR and X-ray Diffraction
9I2I 1.08 Å, X-ray structure of the B1 domain of streptococcal protein G triple mutant T2Q, N8D, and…
6CHE 1.1 Å, Selenomethionine mutant (A34Sem) of protein GB1 examined by X-ray diffraction
6CPZ 1.12 Å, Selenomethionine mutant (I6Sem) of protein GB1 examined by X-ray diffraction
2GI9 1.14 Å, Backbone Conformational Constraints in a Microcrystalline U-15N-Labeled Protein by 3D…
6C9O 1.2 Å, Selenomethionine mutant (V29Sem) of protein GB1 examined by X-ray diffraction
6CTE 1.2 Å, 77Se-NMR probes the protein environment of selenomethionine
6OC7 1.3 Å, HMP42 Fab in complex with Protein G
6NLA 1.34 Å, Crystal structure of de novo designed metal-controlled dimer of B1…
2ON8 1.35 Å, Gbeta1 stabilization by in vitro evolution and computational design
12LO 1.37 Å, X-ray crystal structure of Protein GB1 mutant K13A

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