5NSC: Fc DEKK heterodimer variant

Fc DEKK heterodimer variant. Determined by X-ray diffraction at 2.3 Å resolution. Released 5 Jul 2017.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Homo sapiens, synthetic construct
Chains: 3
Atoms: 3,855
Mol. weight: 56.8 kDa
Released: 5 Jul 2017

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

Secondary structure: helices and β-sheets

5NSC contains 22 α-helices and 42 β-strands across 3 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, 20 β-strands

Element	Residues	Length	Sheet
β-strand	239-243	5	1
α-helix	244-246	3
α-helix	247-251	5
β-strand	258-266	9	1
β-strand	274-279	6	2
β-strand	282-284	3	2
β-strand	288-289	2	1
α-helix	290-292	3
β-strand	293-294	2	1
β-strand	300-307	8	1
α-helix	310-315	6
β-strand	319-324	6	2
β-strand	332-336	5	2
α-helix	339-340	2
β-strand	344	1	3
α-helix	345-346	2
β-strand	347-351	5	4
α-helix	352-354	3
α-helix	355-359	5
β-strand	362-372	11	4
β-strand	373	1	3
β-strand	378-383	6	5
β-strand	386-388	3	5
β-strand	391-393	3	4
α-helix	394-396	3
β-strand	397-398	2	4
β-strand	404-413	10	4
α-helix	414-418	5
β-strand	423-428	6	5
α-helix	433-435	3
β-strand	436-441	6	5

Chain B: 11 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	239-243	5	6
α-helix	244-246	3
α-helix	247-251	5
β-strand	258-267	10	6
β-strand	274-279	6	7
β-strand	282-284	3	7
β-strand	288-289	2	6
α-helix	290-292	3
β-strand	293-294	2	6
β-strand	299-307	9	6
α-helix	310-314	5
β-strand	319-324	6	7
β-strand	332-336	5	7
α-helix	339-340	2
β-strand	344	1	8
α-helix	345-346	2
β-strand	347-351	5	9
α-helix	352-354	3
α-helix	356-359	4
β-strand	362-372	11	9
β-strand	373	1	8
β-strand	378-383	6	10
β-strand	386-388	3	10
β-strand	391-393	3	9
α-helix	394-396	3
β-strand	397-398	2	9
β-strand	404-413	10	9
α-helix	414-418	5
β-strand	423-428	6	10
α-helix	433-435	3
β-strand	437-441	5	10

Chain C: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	11
β-strand	8-12	5	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Putative uncharacterized protein DKFZp686C11235	A	protein	232	Homo sapiens	Q6MZV7 (AlphaFold model)
Putative uncharacterized protein DKFZp686C11235	B	protein	232	Homo sapiens	Q6MZV7 (AlphaFold model)
Fc-III peptide	C	protein	13	synthetic construct

Sequence of entity 1 (A), FASTA

>5NSC_1 Putative uncharacterized protein DKFZp686C11235 (chains A)
EPKSSDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKF
NWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKT
ISKAKGQPREPQVYTKPPSREEMTKNQVSLKCLVKGFYPSDIAVEWESNGQPENNYKTTP
PVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

Sequence of entity 2 (B), FASTA

>5NSC_2 Putative uncharacterized protein DKFZp686C11235 (chains B)
EPKSSDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLEASRTPEVTCVVVDVSHEDPEVKF
NWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKT
ISKAKGQPREPQVYTDPPSREEMTKNQVSLTCEVKGFYPSDIAVEWESNGQPENNYKTTP
PVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNAYTQKSLSLSPGK

Sequence of entity 3 (C), FASTA

>5NSC_3 Fc-III peptide (chains C)
DCAWHLGELVWCT

Primary citation

A new approach for generating bispecific antibodies based on a common light chain format and the stable architecture of human immunoglobulin G1. De Nardis, C., Hendriks, L.J.A., Poirier, E. et al. J Biol Chem (2017) 292:14706-14717. DOI 10.1074/jbc.M117.793497 · PubMed

Other PDB entries of the same protein (UniProt Q6MZV7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7RHO 2.0 Å, Human IgG1 Fc fragment, hinge-free, expressed in E. coli
7LF9 2.2 Å, Structure of Hyperglycosylated Human IgG1 Fc (Fc329)
5NSG 2.22 Å, Fc DEDE homodimer variant
6CHF 2.4 Å, Crystal structure of a Fc fragment LALA mutant (L234A, L235A) of human IgG1 (crystal…
6CJX 2.44 Å, Crystal structure of a Fc fragment LALA mutant (L234A, L235A) of human IgG1 (crystal…
6CJC 2.58 Å, Crystal structure of a fc fragment lala mutant (L234A, L235A) of human IgG1 (crystal…
6N9T 2.58 Å, Structure of a peptide-based photo-affinity cross-linker with Herceptin Fc
7LF5 2.6 Å, Structure of Hyperglycosylated Human IgG1 Fc (Fc267)
7LFN 2.6 Å, Structure of Hyperglycosylated Human IgG1 Fc (Fc267_329)
8F8X 2.6 Å, Crystal structure of Nb.X0 bound to the afucosylated human IgG1 fragment crystal form II
8F8W 2.71 Å, Crystal structure of Nb.X0 bound to the afucosylated human IgG1 fragment crystal form I
9IUJ 2.78 Å, Integrin alpha-v beta-3 in complex with rhodostomin

Browse structure collections

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