6Z6Z: Neutrophil gelatinase-associated lipocalin

Crystal structure of an Anticalin directed towards colchicine without ligand. Determined by X-ray diffraction at 1.78 Å resolution. Released 9 Jun 2021.

Method: X-ray diffraction
Resolution: 1.78 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,466
Mol. weight: 21.54 kDa
Ligands: CA
Released: 9 Jun 2021

Explore 6Z6Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Z6Z contains 7 α-helices and 9 β-strands across 1 chain. 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: 7 helices, 9 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	48-51	4
β-strand	53-58	6	1
β-strand	64-69	6	1
α-helix	70	1
β-strand	78-85	8	1
β-strand	91-94	4	1
β-strand	106-113	8	1
β-strand	118-125	8	1
β-strand	133-139	7	1
α-helix	146-158	13
α-helix	163-165	3
β-strand	166-167	2	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neutrophil gelatinase-associated lipocalin	A	protein	187	Homo sapiens	P80188 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6Z6Z_1 Neutrophil gelatinase-associated lipocalin (chains A)
MQDSTSDLIPAPPLSKVPLQQNFQDNQFHGKWYVVGVAGNGFLREDKDPIKMAATIYELK
EDKSYNVTFMKFPMKKCQYMTDTLVPGSQPGEFTLGNIKSEPGYTSWLVRVVSTNYNQHA
MVFFKAVQQNREDFFITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCIDGS
AHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

Primary citation

Structural rearrangement in the ligand pocket of Colchicalin upon Colchicine binding. Ilyukhina, E., 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…
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…
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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