8ZCK: Immunoglobulin gamma-1 heavy chain

Serial Femtosecond Crystallography Structure of Fc Fragment of Human IgG1 from Biosimilar VEGF-Trap. Determined by X-ray diffraction at 2.0 Å resolution. Released 8 May 2024.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,670
Mol. weight: 50.15 kDa
Released: 8 May 2024

Explore 8ZCK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ZCK contains 20 α-helices and 39 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, 19 β-strands

Element	Residues	Length	Sheet
β-strand	224-228	5	1
α-helix	229-231	3
α-helix	232-236	5
β-strand	243-251	9	1
β-strand	259-264	6	2
β-strand	267-269	3	2
β-strand	273-279	7	1
β-strand	285-292	8	1
α-helix	295-300	6
β-strand	304-309	6	2
β-strand	317-321	5	2
α-helix	323-325	3
β-strand	329	1	3
α-helix	330-331	2
β-strand	332-336	5	4
α-helix	337-339	3
α-helix	340-344	5
β-strand	347-357	11	4
β-strand	358	1	3
β-strand	363-368	6	5
β-strand	371-372	2	5
β-strand	376-378	3	4
α-helix	379-381	3
β-strand	382-383	2	4
β-strand	389-398	10	4
α-helix	399-404	6
β-strand	408-413	6	5
α-helix	418-420	3
β-strand	421-426	6	5

Chain B: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	224-228	5	6
α-helix	229-231	3
α-helix	232-236	5
β-strand	243-252	10	6
β-strand	259-264	6	7
β-strand	267-269	3	7
β-strand	273-274	2	6
α-helix	275-277	3
β-strand	278-279	2	6
β-strand	284-292	9	6
α-helix	295-299	5
β-strand	304-309	6	7
β-strand	317-321	5	7
α-helix	323-325	3
β-strand	329	1	8
β-strand	332-336	5	9
α-helix	337-339	3
α-helix	340-344	5
β-strand	347-357	11	9
β-strand	358	1	8
β-strand	363-368	6	10
β-strand	371-372	2	10
β-strand	376-378	3	9
α-helix	379-381	3
β-strand	382-383	2	9
β-strand	389-398	10	9
α-helix	399-403	5
β-strand	408-413	6	10
α-helix	418-420	3
β-strand	422-426	5	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin gamma-1 heavy chain	A, B	protein	208	Homo sapiens	P0DOX5 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8ZCK_1 Immunoglobulin gamma-1 heavy chain (chains A, B)
GPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQY
NSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRD
ELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSR
WQQGNVFSCSVMHEALHNHYTQKSLSLS

Primary citation

Experimental and Computational Insights into the Structural Dynamics of the Fc Fragment of IgG1 Subtype from Biosimilar VEGF-Trap. Destan, E., Turkut, E., Aldeniz, A. et al. Small Struct (2025). DOI 10.1002/sstr.202400680

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…

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