5N48: Anticalin N9B

Structure of Anticalin N9B in complex with extra-domain B of human oncofetal fibronectin. Determined by X-ray diffraction at 1.6 Å resolution. Released 14 Feb 2018.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,513
Mol. weight: 65.99 kDa
Released: 14 Feb 2018

Explore 5N48 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5N48 contains 22 α-helices and 34 β-strands across 4 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: 7 helices, 9 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	1
β-strand	50-58	9	1
β-strand	64-72	9	1
β-strand	75-85	11	1
β-strand	91-94	4	1
α-helix	95-96	2
β-strand	105-113	9	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	169-172	4

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	1267-1270	4
β-strand	1274-1276	3	2
β-strand	1282-1286	5	2
α-helix	1288-1290	3
β-strand	1295-1304	10	3
β-strand	1312-1317	6	3
β-strand	1322-1326	5	2
α-helix	1328-1329	2
β-strand	1333-1342	10	3
β-strand	1345-1346	2	3
α-helix	1347-1349	3
β-strand	1350-1355	6	3

Chain C: 7 helices, 9 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	4
α-helix	41-44	4
β-strand	50-58	9	4
β-strand	64-72	9	4
β-strand	75-85	11	4
β-strand	91-93	3	4
β-strand	105-113	9	4
β-strand	118-127	10	4
β-strand	130-139	10	4
α-helix	146-158	13
α-helix	163-165	3
β-strand	166-167	2	4
α-helix	169-171	3

Chain D: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	1266-1270	5
β-strand	1274-1276	3	5
β-strand	1282-1286	5	5
α-helix	1288-1290	3
β-strand	1295-1304	10	6
β-strand	1312-1317	6	6
β-strand	1322-1326	5	5
α-helix	1328-1329	2
β-strand	1333-1342	10	6
β-strand	1345-1346	2	6
α-helix	1347-1349	3
β-strand	1350-1355	6	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neutrophil gelatinase-associated lipocalin	A, C	protein	188	Homo sapiens	P80188 (AlphaFold model)
Fibronectin	B, D	protein	106	Homo sapiens	P02751 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5N48_1 Neutrophil gelatinase-associated lipocalin (chains A, C)
QDSTSDLIPAPPLSKVPLQQNFQDNQFHGKWYVVGRAGNMRLREDKDPAKMVATIYELKE
DKSYNVTKVMFQRKKCKYMINTFVPGSQPGEFTLGAIKSPPGPTSTLVRVVSTNYNQHAM
VFFKHVFQNREYFHITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCIDGSA
WSHPQFEK

Sequence of entity 2 (B, D), FASTA

>5N48_2 Fibronectin (chains B, D)
MASRGSHHHHHHGAEVPQLTDLSFVDITDSSIGLRWTPLNSSTIIGYRITVVAAGEGIPI
FEDFVDSSVGYYTVTGLEPGIDYDISVITLINGGESAPTTLTQQTA

Primary citation

Anticalins Reveal High Plasticity in the Mode of Complex Formation with a Common Tumor Antigen. Schiefner, A., Gebauer, M., Richter, A. et al. Structure (2018) 26:649-656.e3. DOI 10.1016/j.str.2018.02.003 · 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…
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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