3UPC: Heavy chain variable domain

A general strategy for the generation of human antibody variable domains with increased aggregation resistance. Determined by X-ray diffraction at 2.8 Å resolution. Released 20 Jun 2012.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 10
Atoms: 8,217
Mol. weight: 122.43 kDa
Released: 20 Jun 2012

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

Secondary structure: helices and β-sheets

3UPC contains 23 α-helices and 105 β-strands across 10 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, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-12	3	2
β-strand	18-24	7	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	58-60	3	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	110-114	5	2

Chain B: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	3
β-strand	10-12	3	2
β-strand	18-24	7	3
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	58-60	3	2
β-strand	68-73	6	3
α-helix	74-76	3
β-strand	78-83	6	3
α-helix	88-90	3
β-strand	92-98	7	2
β-strand	110-114	5	2

Chain C: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	4
β-strand	11-12	2	5
β-strand	18-24	7	4
α-helix	29-31	3
β-strand	34-39	6	6
β-strand	45-51	7	6
β-strand	58-60	3	6
β-strand	68-73	6	4
β-strand	78-83	6	4
α-helix	88-90	3
β-strand	92-98	7	6
β-strand	110-112	3	6
β-strand	113-114	2	7

Chain D: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	8
β-strand	11-12	2	7
β-strand	18-24	7	8
α-helix	29-31	3
β-strand	34-39	6	6
β-strand	45-51	7	6
β-strand	58-60	3	6
β-strand	68-73	6	8
β-strand	78-83	6	8
α-helix	88-90	3
β-strand	92-98	7	6
α-helix	105-107	3
β-strand	110-112	3	6
β-strand	113-114	2	5

Chains E and F: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	9
β-strand	10-12	3	10
β-strand	18-24	7	9
α-helix	29-31	3
β-strand	34-39	6	10
β-strand	45-51	7	10
β-strand	58-60	3	10
β-strand	68-73	6	9
β-strand	78-83	6	9
α-helix	88-90	3
β-strand	92-98	7	10
β-strand	110-112	3	10
β-strand	113-114	2	11

Chain G: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	15
β-strand	10-12	3	16
β-strand	18-24	7	15
α-helix	29-31	3
β-strand	34-39	6	16
β-strand	45-51	7	16
β-strand	58-60	3	16
β-strand	68-73	6	15
β-strand	78-83	6	15
α-helix	88-90	3
β-strand	92-98	7	16
α-helix	105-107	3
β-strand	110-112	3	16
β-strand	113	1	17

Chain H: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	18
β-strand	11	1	17
β-strand	18-24	7	18
α-helix	29-31	3
β-strand	34-39	6	16
β-strand	45-51	7	16
β-strand	58-60	3	16
β-strand	68-73	6	18
β-strand	78-83	6	18
α-helix	88-90	3
β-strand	92-98	7	16
β-strand	110-114	5	16

Chains I and J: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	19
β-strand	11-12	2	11
β-strand	18-24	7	19
α-helix	29-31	3
β-strand	34-39	6	10
β-strand	45-51	7	10
β-strand	58-60	3	10
β-strand	68-73	6	19
β-strand	78-83	6	19
α-helix	88-90	3
β-strand	92-98	7	10
β-strand	110-114	5	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
heavy chain variable domain	A, B, C, D, E, F, G, H, I, J	protein	113	Homo sapiens	P01764 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J), FASTA

>3UPC_1 heavy chain variable domain (chains A, B, C, D, E, F, G, H, I, J)
QLLESGGGLVQPGGSLRLSCAASGFTFSDEDMSWVRQAPGKGLEWVSAISGSGGSTYYAD
SVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKSYGAFDYWGQGTLVTVS

Primary citation

General strategy for the generation of human antibody variable domains with increased aggregation resistance. Dudgeon, K., Rouet, R., Kokmeijer, I. et al. Proc Natl Acad Sci U S A (2012) 109:10879-10884. DOI 10.1073/pnas.1202866109 · PubMed

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

3ZHD 1.96 Å, The crystal structure of single domain antibody 8-4 scaffold.
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
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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