3ZHD: Single domain antibody 8-4 scaffold

The crystal structure of single domain antibody 8-4 scaffold. Determined by X-ray diffraction at 1.96 Å resolution. Released 8 Jan 2014.

Method: X-ray diffraction
Resolution: 1.96 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 2,066
Mol. weight: 27.53 kDa
Released: 8 Jan 2014

Explore 3ZHD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3ZHD contains 6 α-helices and 22 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: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	46-51	6	2
β-strand	57-60	4	2
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-98	7	2
β-strand	99	1	3
β-strand	103	1	3
α-helix	106-108	3
β-strand	113-117	5	2

Chain B: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	4
β-strand	10-12	3	2
β-strand	18-25	8	4
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	46-51	6	2
β-strand	57-60	4	2
β-strand	68-73	6	4
β-strand	78-83	6	4
α-helix	88-90	3
β-strand	92-98	7	2
α-helix	106-108	3
β-strand	113-117	5	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MG8-4 scaffold antibody	A, B	protein	127	HOMO SAPIENS	P01764 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3ZHD_1 MG8-4 SCAFFOLD ANTIBODY (chains A, B)
EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYAMGWVRQAPGKGPEVVSLISGSGGSTWY
DDSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARHAPSTEAPDYWGQGTLVTVSSL
EHHHHHH

Primary citation

Directed Evolution of Human Heavy Chain Variable Domain (Vh) Using in Vivo Protein Fitness Filter. Kim, D., Song, H., Nam, H.J. et al. PLoS One (2014) 9:98178. DOI 10.1371/JOURNAL.PONE.0098178 · PubMed

Other PDB entries of the same protein (UniProt P01764 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3ZHK 1.96 Å, The crystal structure of single domain antibody 2x1 scaffold
1OHQ 2.0 Å, Crystal structure of HEL4, a soluble human VH antibody domain resistant to aggregation
3ZHL 2.47 Å, The crystal structure of single domain antibody 8-14 scaffold
3UPC 2.8 Å, A general strategy for the generation of human antibody variable domains with increased…
4KFZ 2.8 Å, Crystal structure of LMO2 and anti-LMO2 VH complex
9N7Q 3.18 Å, H1 hemagglutinin (A/Michigan/45/2015) in complex with anchor-targeting Fab ST15

Browse structure collections

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