6Z2C: Engineered lipocalin C3A5

Engineered lipocalin C3A5 in complex with a transition state analog. Determined by X-ray diffraction at 1.8 Å resolution. Released 26 May 2021.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,718
Mol. weight: 66.91 kDa
Ligands: Q5E
Released: 26 May 2021

Explore 6Z2C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Z2C contains 21 α-helices and 33 β-strands across 3 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.

Chains A, B and C: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	1
α-helix	8-12	5
α-helix	13-15	3
α-helix	24-27	4
β-strand	29-38	10	2
β-strand	40	1	1
α-helix	47-50	4
β-strand	51-58	8	2
β-strand	64-72	9	2
β-strand	75-85	11	2
β-strand	91-94	4	2
β-strand	107-113	7	2
β-strand	118-127	10	2
β-strand	130-139	10	2
α-helix	146-158	13
α-helix	163-165	3
β-strand	166-167	2	2
α-helix	169-171	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neutrophil gelatinase-associated lipocalin	A, B, C	protein	188	Homo sapiens	P80188 (AlphaFold model)

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

>6Z2C_1 Neutrophil gelatinase-associated lipocalin (chains A, B, C)
QDSTSDLIPAPPLSKVPLQQNFQDNQFHGKWYVVGMAGNGDLREDKDPYKMRATIYELKE
DKSYNVTWVWFLPKKCKYFINTFVPGSQPGEFTLGLIKSYPGQTSLLVRVVSTNYNQHAM
VFFKTVIQNRERFYITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCIDGSA
WSHPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
Q5E	1,7,8,9,10,10-hexachloro-4-carboxypentyl-4-aza-tricyclo[5.2.1.0(2,6)]dec-8-ene-…	C15 H13 Cl6 N O4	3

Primary citation

Structure of an engineered lipocalin that catalyzes a Diels-Alder reaction. Eichinger, A., Skerra, A. To be published.

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…
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…
3DSZ 2.0 Å, Engineered human lipocalin 2 in complex with Y-DTPA
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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