6S8V: High affinity Anticalin P3D11

Structure of the high affinity Anticalin P3D11 in complex with the human CD98 heavy chain ectodomain. Determined by X-ray diffraction at 1.8 Å resolution. Released 4 Mar 2020.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,265
Mol. weight: 137.42 kDa
Released: 4 Mar 2020

Explore 6S8V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6S8V contains 62 α-helices and 60 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, 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	1
β-strand	50	1	2
β-strand	53-58	6	1
β-strand	64-71	8	1
β-strand	76-85	10	1
β-strand	91-94	4	1
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	1
β-strand	170	1	2
α-helix	171	1

Chain B: 23 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	117-119	3
β-strand	123-126	4	3
α-helix	129-133	5
α-helix	140-144	5
α-helix	147-152	6
β-strand	157-160	4	3
β-strand	164-166	3	4
β-strand	174-179	6	4
α-helix	181-183	3
α-helix	186-198	13
β-strand	202-206	5	3
α-helix	222-239	18
β-strand	243-246	4	3
α-helix	249-251	3
α-helix	255-269	15
β-strand	274-278	5	3
α-helix	284-291	8
β-strand	298-300	3	3
α-helix	311-324	14
β-strand	331-332	2	5
α-helix	340-342	3
α-helix	346-348	3
α-helix	349-356	8
β-strand	362-363	2	5
β-strand	364-366	3	3
α-helix	369-371	3
α-helix	375-377	3
α-helix	386-388	3
α-helix	404-406	3
α-helix	408-412	5
α-helix	418-431	14
α-helix	433-437	5
β-strand	439-442	4	6
β-strand	449-455	7	6
β-strand	461-467	7	6
β-strand	473-474	2	7
α-helix	479-481	3
β-strand	491-497	7	6
β-strand	507-509	3	6
α-helix	510-512	3
β-strand	514-515	2	7
β-strand	520-525	6	6

Chain C: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	9-12	4
α-helix	13-15	3
β-strand	29-38	10	8
β-strand	50	1	9
β-strand	53-58	6	8
β-strand	64-71	8	8
β-strand	76-85	10	8
β-strand	91-94	4	8
β-strand	105-113	9	8
β-strand	118-127	10	8
β-strand	130-139	10	8
α-helix	146-158	13
α-helix	163-165	3
β-strand	166-167	2	8
α-helix	169	1
β-strand	170	1	9
α-helix	171	1

Chain D: 26 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	112-114	3
α-helix	117-120	4
β-strand	123-126	4	10
α-helix	129-133	5
α-helix	140-144	5
α-helix	147-152	6
β-strand	157-160	4	10
β-strand	164-166	3	11
β-strand	174-179	6	11
α-helix	181-183	3
α-helix	186-198	13
β-strand	202-206	5	10
α-helix	222-238	17
β-strand	243-246	4	10
α-helix	249-251	3
α-helix	255-269	15
β-strand	274-278	5	10
α-helix	284-291	8
β-strand	298-300	3	10
α-helix	311-324	14
β-strand	331-332	2	12
α-helix	340-342	3
α-helix	346-348	3
α-helix	349-356	8
β-strand	362-363	2	12
β-strand	364-366	3	10
α-helix	369-371	3
α-helix	375-377	3
α-helix	386-388	3
α-helix	404-406	3
α-helix	408-412	5
α-helix	418-431	14
α-helix	433-436	4
β-strand	440-442	3	13
α-helix	443-444	2
β-strand	449-454	6	13
α-helix	460	1
β-strand	461-467	7	13
β-strand	473-475	3	14
α-helix	479-481	3
β-strand	491-497	7	13
β-strand	507-509	3	13
α-helix	510-512	3
β-strand	513-515	3	14
β-strand	520-525	6	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neutrophil gelatinase-associated lipocalin	A, C	protein	186	Homo sapiens	P80188 (AlphaFold model)
4F2 cell-surface antigen heavy chain	B, D	protein	431	Homo sapiens	P08195 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6S8V_1 Neutrophil gelatinase-associated lipocalin (chains A, C)
QDSTSDLIPAPPLSKVPLQQNFQDNQFHGKWYVVGRAGNTGLREDKDPGKMFATIYELKE
DKSYNVTYVWFGQKKCMYSIGTFVPGSQPGEFTLGNIKSAPGRTSWLVRVVSTNYNQHAM
VFFKSVTQNREGFAITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCIDGSA
HHHHHH

Sequence of entity 2 (B, D), FASTA

>6S8V_2 4F2 cell-surface antigen heavy chain (chains B, D)
ASWSHPQFEKGAELPAQKWWHTGALYRIGDLQAFQGHGAGNLAGLKGRLDYLSSLKVKGL
VLGPIHKNQKDDVAQTDLLQIDPNFGSKEDFDSLLQSAKKKSIRVILDLTPNYRGENSWF
STQVDTVATKVKDALEFWLQAGVDGFQVRDIENLKDASSFLAEWQNITKGFSEDRLLIAG
TNSSDLQQILSLLESNKDLLLTSSYLSDSGSTGEHTKSLVTQYLNATGNRWCSWSLSQAR
LLTSFLPAQLLRLYQLMLFTLPGTPVFSYGDEIGLDAAALPGQPMEAPVMLWDESSFPDI
PGAVSANMTVKGQSEDPGSLLSLFRRLSDQRSKERSLLHGDFHAFSAGPGLFSYIRHWDQ
NERFLVVLNFGDVGLSAGLQASDLPASASLPAKADLLLSTQPGREEGSPLELERLKLEPH
EGLLLRFPYAA

Primary citation

Development of a high affinity Anticalin®directed against human CD98hc for theranostic applications. Deuschle, F.C., Morath, V., Schiefner, A. et al. Theranostics (2020) 10:2172-2187. DOI 10.7150/thno.38968 · 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
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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