6GQZ: Neutrophil gelatinase-associated lipocalin

Petrobactin-binding engineered lipocalin without ligand. Determined by X-ray diffraction at 1.4 Å resolution. Released 15 Aug 2018.

Method: X-ray diffraction
Resolution: 1.4 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,288
Mol. weight: 40.27 kDa
Released: 15 Aug 2018

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

Secondary structure: helices and β-sheets

6GQZ contains 21 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: 11 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
α-helix	13-15	3
α-helix	24-27	4
β-strand	29-38	10	1
α-helix	46-49	4
β-strand	50	1	2
α-helix	51	1
β-strand	53-58	6	1
α-helix	63	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	9-12	4
α-helix	13-15	3
α-helix	24-27	4
β-strand	29-38	10	3
α-helix	46-49	4
β-strand	50	1	4
α-helix	51	1
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
Neutrophil gelatinase-associated lipocalin	A, B	protein	174	Homo sapiens	P80188 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6GQZ_1 Neutrophil gelatinase-associated lipocalin (chains A, B)
SDLIPAPPLSKVPLQQNFQDNQFHGKWYVVGFAENIQQREDKDPPKMIATIYELKEDKSY
NVTNVASNWEKCTYRIKTFVPGSQPGEFTLGEIKSRPGMTSYLVRVVSTNYNQHAMVFFK
TVVQNREKFWITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCIDG

Primary citation

Reprogramming Human Siderocalin To Neutralize Petrobactin, the Essential Iron Scavenger of Anthrax Bacillus. Dauner, M., Eichinger, A., Lucking, G. et al. Angew Chem Int Ed Engl (2018) 57:14619-14623. DOI 10.1002/anie.201807442 · PubMed

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

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…
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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