6QMU: Neutrophil gelatinase-associated lipocalin

A tetrahedral boronic acid diester formed by a non-natural amino acid in the ligand pocket of an engineered lipocalin. Determined by X-ray diffraction at 1.98 Å resolution. Released 28 Aug 2019.

Method: X-ray diffraction
Resolution: 1.98 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,152
Mol. weight: 44.02 kDa
Ligands: ZCQ
Released: 28 Aug 2019

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

Secondary structure: helices and β-sheets

6QMU contains 23 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: 12 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
α-helix	13-15	3
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
α-helix	59	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
α-helix	184-185	2

Chain B: 11 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	7-12	6
α-helix	13-15	3
β-strand	29-38	10	3
α-helix	48-49	2
β-strand	50	1	4
α-helix	51	1
β-strand	53-58	6	3
α-helix	59	1
α-helix	63	1
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	188	Homo sapiens	P80188 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6QMU_1 Neutrophil gelatinase-associated lipocalin (chains A, B)
QDSTSDLIPAPPLSKVPLQQNFQDNQFHGKWYVVGFAGNAILREDKDPQKMFATIYELKE
DKSYNVTSVLFRKKKCDYWIRTFVPGSQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAM
VFFKWVSQNREYFNITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCIDGSA
WSHPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
ZCQ	3-nitrophenol	C6 H5 N O3	2

Primary citation

A Tetrahedral Boronic Acid Diester Formed by an Unnatural Amino Acid in the Ligand Pocket of an Engineered Lipocalin. Sommer, C.A., Eichinger, A., Skerra, A. Chembiochem (2020) 21:469-472. DOI 10.1002/cbic.201900405 · 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
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

Browse structure collections

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