3DSZ: Engineered human lipocalin 2

Engineered human lipocalin 2 in complex with Y-DTPA. Determined by X-ray diffraction at 2.0 Å resolution. Released 19 May 2009.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,216
Mol. weight: 44.3 kDa
Ligands: YT3, LIZ
Released: 19 May 2009

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

Secondary structure: helices and β-sheets

3DSZ contains 20 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: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	9-12	4
α-helix	13-15	3
α-helix	24-27	4
β-strand	29-38	10	1
α-helix	48-49	2
β-strand	50	1	2
α-helix	51	1
β-strand	53-58	6	1
β-strand	64-72	9	1
β-strand	75-85	11	1
β-strand	91-94	4	1
α-helix	97-99	3
β-strand	103-113	11	1
β-strand	118-127	10	1
β-strand	130-139	10	1
α-helix	146-158	13
α-helix	163-165	3
β-strand	166-167	2	1
α-helix	169	1
β-strand	170	1	2
α-helix	171	1

Chain B: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	8-12	5
α-helix	13-15	3
α-helix	24-27	4
β-strand	29-38	10	3
α-helix	43-46	4
α-helix	48-49	2
β-strand	50	1	4
β-strand	53-58	6	3
β-strand	64-72	9	3
β-strand	75-85	11	3
β-strand	91-94	4	3
α-helix	97-99	3
β-strand	103-113	11	3
β-strand	118-127	10	3
β-strand	130-139	10	3
α-helix	146-158	13
α-helix	163-165	3
β-strand	166-167	2	3
α-helix	169	1
β-strand	170	1	4
α-helix	171	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
engineered human lipocalin 2	A, B	protein	186	Homo sapiens	P80188 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3DSZ_1 engineered human lipocalin 2 (chains A, B)
QDSTSDLIPAPPLSKVPLQQNFQDNQFHGKWYQVGRAGNAALREDKDPQKMTAQIYELKE
DKSYNVTAVRFRKKKCDYLTMTFVPGSQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAM
VFFKKVSQNREYFSITLLGRTKELASELKENFIRFSKSLGLPENHIVFPVPIDQCIDGSA
HHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
YT3	Yttrium (III) ion	Y	2
LIZ	N-{(1S,2S)-2-[bis(carboxymethyl)amino]cyclohexyl}-N-{(2R)-2-[bis(carboxymethyl)…	C30 H45 N5 O13 S	2

Primary citation

High-affinity recognition of lanthanide(III) chelate complexes by a reprogrammed human lipocalin 2. Kim, H.J., Eichinger, A., Skerra, A. J Am Chem Soc (2009) 131:3565-3576. DOI 10.1021/ja806857r · PubMed

Other PDB entries of the same protein (UniProt P80188 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6GQZ 1.4 Å, Petrobactin-binding engineered lipocalin without ligand
4MVK 1.5 Å, Crystal structure of an engineered lipocalin (Anticalin US7) in complex with the…
5N48 1.6 Å, Structure of Anticalin N9B in complex with extra-domain B of human oncofetal fibronectin
4MVI 1.7 Å, Crystal structure of an engineered lipocalin (Anticalin US7) in complex with the…
6Z6Z 1.78 Å, Crystal structure of an Anticalin directed towards colchicine without ligand
6S8V 1.8 Å, Structure of the high affinity Anticalin P3D11 in complex with the human CD98 heavy…
6Z2C 1.8 Å, Engineered lipocalin C3A5 in complex with a transition state analog
4IAX 1.9 Å, Engineered human lipocalin 2 (CL31) in complex with Y-DTPA
6QMU 1.98 Å, A tetrahedral boronic acid diester formed by a non-natural amino acid in the ligand…
5MHH 2.0 Å, Crystal structure of engineered human lipocalin 2 carrying p-boronophenylalanine at…
8UYN 2.0 Å, Fundamental Characterization of Chelated and Crystallized Actinium in a Macromolecular…
4ZHC 2.04 Å, Siderocalin-mediated recognition and cellular uptake of actinides

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