5HDO: PDB entry 5HDO

Crystal structure of a nanobody raised against urokinase-type plasminogen activator. Determined by X-ray diffraction at 2.16 Å resolution. Released 1 Jun 2016.

Method: X-ray diffraction
Resolution: 2.16 Å
Organism: Camelus dromedarius
Chains: 4
Atoms: 4,219
Mol. weight: 54.92 kDa
Released: 1 Jun 2016

Explore 5HDO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5HDO contains 9 α-helices and 45 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: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
β-strand	34-39	6	2
β-strand	46-51	6	2
β-strand	58-60	3	2
α-helix	62-64	3
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	116-117	2	2
β-strand	121-125	5	2

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	3
β-strand	10-13	4	2
β-strand	18-25	8	3
β-strand	34-39	6	2
β-strand	46-51	6	2
β-strand	58-60	3	2
α-helix	62-64	3
β-strand	68-73	6	3
β-strand	78-83	6	3
α-helix	88-90	3
β-strand	92-98	7	2
α-helix	112-113	2
β-strand	116-117	2	2
β-strand	121-126	6	2

Chain C: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	4
β-strand	10-13	4	5
β-strand	18-25	8	4
β-strand	34-39	6	5
β-strand	46-51	6	5
β-strand	58-60	3	5
β-strand	68-73	6	4
β-strand	78-83	6	4
α-helix	88-90	3
β-strand	92-98	7	5
β-strand	116-117	2	5
β-strand	121-126	6	5

Chain D: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	10-13	4	7
β-strand	18-25	8	6
β-strand	34-39	6	7
β-strand	46-51	6	7
β-strand	58-60	3	7
α-helix	62-64	3
β-strand	68-73	6	6
β-strand	78-83	6	6
α-helix	88-90	3
β-strand	92-98	7	7
α-helix	111-113	3
β-strand	116-117	2	7
β-strand	118	1	6
β-strand	121-126	6	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Anti-HCV NS3/4A serine protease immoglobulin heavy chain	A, B, C, D	protein	128	Camelus dromedarius	A0A0F6YEF6 (AlphaFold model)

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

>5HDO_1 Anti-HCV NS3/4A serine protease immoglobulin heavy chain (chains A, B, C, D)
QVQLQESGGGLVQAGGSLRLSCAASGFTLDSYAIGWFRQAPGKEREGVSCISASGGSTNY
ADSVKGRFTISRDNAKNTVYLQMNSLKSEDTAVYYCAADHPGLCTSESGRRRYLEVWGQG
TQVTVSSA

Primary citation

A Camelid-derived Antibody Fragment Targeting the Active Site of a Serine Protease Balances between Inhibitor and Substrate Behavior. Kromann-Hansen, T., Oldenburg, E., Yung, K.W. et al. J Biol Chem (2016) 291:15156-15168. DOI 10.1074/jbc.M116.732503 · PubMed

Other PDB entries of the same protein (UniProt A0A0F6YEF6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8XT9 3.1 Å, structure of LGR4

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