6YSC: Glycosylated knob-hole/dummy fc fragment

Glycosylated knob-hole/dummy fc fragment. Determined by X-ray diffraction at 2.05 Å resolution. Released 14 Oct 2020.

Method: X-ray diffraction
Resolution: 2.05 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,573
Mol. weight: 55.51 kDa
Released: 14 Oct 2020

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

Secondary structure: helices and β-sheets

6YSC contains 19 α-helices and 41 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: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	239-243	5	1
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	310-314	5
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	355-357	3
β-strand	362-372	11	4
β-strand	373	1	3
β-strand	378-383	6	5
β-strand	386-387	2	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	437-441	5	5

Chain B: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	239-243	5	6
α-helix	244-246	3
α-helix	247-251	5
β-strand	258-264	7	6
β-strand	276-279	4	7
β-strand	282-284	3	7
β-strand	288-289	2	6
β-strand	293-294	2	8
β-strand	300-301	2	8
β-strand	302-307	6	6
α-helix	310-314	5
β-strand	319-323	5	7
α-helix	331	1
β-strand	332-336	5	7
α-helix	338-340	3
β-strand	344	1	9
α-helix	345-346	2
β-strand	347-351	5	10
β-strand	362-372	11	10
β-strand	373	1	9
β-strand	378-383	6	11
β-strand	386-387	2	11
β-strand	391-393	3	10
α-helix	394-396	3
β-strand	397-398	2	10
β-strand	404-413	10	10
α-helix	414-419	6
β-strand	423-428	6	11
α-helix	433-435	3
β-strand	437-441	5	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin gamma-1 heavy chain	A	protein	227	Homo sapiens	P0DOX5 (AlphaFold model)
Immunoglobulin gamma-1 heavy chain	B	protein	241	Homo sapiens	P0DOX5 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6YSC_1 Immunoglobulin gamma-1 heavy chain (chains A)
DKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVD
GVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAK
GQPREPQVYTLPPCRDELTKNQVSLWCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDS
DGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

Sequence of entity 2 (B), FASTA

>6YSC_2 Immunoglobulin gamma-1 heavy chain (chains B)
DKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVD
GVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAK
GQPREPQVYTLPPSRDKLTKNQVSLSCAVKGFYPSDIAVEWESNGQPENNYKTTPPVLDS
DGSFFLVSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGKGGGGSHHHHHHHH
C

Primary citation

Format chain exchange (FORCE) for high-throughput generation of bispecific antibodies in combinatorial binder-format matrices. Dengl, S., Mayer, K., Bormann, F. et al. Nat Commun (2020) 11:4974-4974. DOI 10.1038/s41467-020-18477-7 · PubMed

Other PDB entries of the same protein (UniProt P0DOX5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6YT7 1.55 Å, Glycosylated knob/dummy-hole fc fragment
6YTB 1.65 Å, Glycosylated knob/dummy-hole/dummy fc fragment
6ARP 1.7 Å, Structure of a mutant Cetuximab Fab fragment
1N0X 1.8 Å, Crystal Structure of a Broadly Neutralizing Anti-HIV-1 Antibody in Complex with a…
6UOE 1.8 Å, 3-25 Fab germline-reversion variant bound to an HCMV gB-derived peptide
8ECV 1.81 Å, Bovine Fab 2F12
6G1E 1.88 Å, BEAT Fc with improved heterodimerization (Q3A-D84.4Q)
5W5L 1.9 Å, Crystal structure of human IgG1-Sigma Fc fragment
6UBI 1.9 Å, N123-VRC34.05 HIV neutralizing antibody in complex with HIV fusion peptide residue 512-519
6DKJ 1.95 Å, human GIPR ECD and Fab complex
6MSY 2.0 Å, Anti-HIV-1 Fab Fab 2G12 + Man4 re-refinement
6UGW 2.0 Å, Crystal structure of the Fc fragment of PF06438179/GP1111 an infliximab biosimilar in a…

Browse structure collections

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