4ZHH: Neutrophil gelatinase-associated lipocalin

Siderocalin-mediated recognition and cellular uptake of actinides. Determined by X-ray diffraction at 2.04 Å resolution. Released 5 Aug 2015.

Method: X-ray diffraction
Resolution: 2.04 Å
Organism: Homo sapiens
Chains: 6
Atoms: 9,430
Mol. weight: 130.83 kDa
Ligands: 4OL, SM
Released: 5 Aug 2015

Explore 4ZHH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4ZHH contains 60 α-helices and 68 β-strands across 6 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 and D: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	8-12	5
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	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: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	1
α-helix	8-12	5
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
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

Chain C: 11 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	5
α-helix	8-12	5
α-helix	13-15	3
α-helix	24-27	4
β-strand	29-38	10	6
α-helix	48-49	2
β-strand	50	1	7
α-helix	51	1
β-strand	53-58	6	6
α-helix	63	1
β-strand	64-72	9	6
β-strand	75-85	11	6
β-strand	91-94	4	6
α-helix	97-99	3
β-strand	103-113	11	6
β-strand	118-127	10	6
β-strand	130-139	10	6
α-helix	146-158	13
α-helix	163-165	3
β-strand	166-167	2	6
α-helix	169	1
β-strand	170	1	7
α-helix	171	1

Chains E and F: 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	9
α-helix	48-49	2
β-strand	50	1	10
α-helix	51	1
β-strand	53-58	6	9
β-strand	64-72	9	9
β-strand	75-85	11	9
β-strand	91-94	4	9
α-helix	97-99	3
β-strand	103-113	11	9
β-strand	118-127	10	9
β-strand	130-139	10	9
α-helix	146-158	13
α-helix	163-165	3
β-strand	166-167	2	9
α-helix	169	1
β-strand	170	1	10
α-helix	171	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neutrophil gelatinase-associated lipocalin	A, B, C, D, E, F	protein	180	Homo sapiens	P80188 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>4ZHH_1 Neutrophil gelatinase-associated lipocalin (chains A, B, C, D, E, F)
GSQDSTSDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYEL
KEDKSYNVTSVLFRKKKCDYWIRTFVPGSQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQH
AMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCIDG

Ligands and cofactors

ID	Name	Formula	Copies
4OL	N,N'-butane-1,4-diylbis[1-hydroxy-N-(3-{[(1-hydroxy-6-oxo-1,6-dihydropyridin-2-…	C34 H38 N8 O12	6
SM	Samarium (III) ion	Sm	6

Water and common crystallization additives (SO4, CL, GOL) are not listed.

Primary citation

Siderocalin-mediated recognition, sensitization, and cellular uptake of actinides. Allred, B.E., Rupert, P.B., Gauny, S.S. et al. Proc Natl Acad Sci U S A (2015) 112:10342-10347. DOI 10.1073/pnas.1508902112 · 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…
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…

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