5W5L: Human IgG1-Sigma Fc fragment

Crystal structure of human IgG1-Sigma Fc fragment. Determined by X-ray diffraction at 1.9 Å resolution. Released 13 Sept 2017.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,772
Mol. weight: 53.16 kDa
Released: 13 Sept 2017

Explore 5W5L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5W5L contains 22 α-helices and 40 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	240-243	4	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	310-314	5
β-strand	319-324	6	2
β-strand	332-336	5	2
α-helix	338-340	3
β-strand	344	1	3
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	386-387	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	436-441	6	5

Chain B: 12 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	237-239	3
β-strand	240-243	4	6
α-helix	244-246	3
α-helix	247-251	5
β-strand	258-266	9	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	300-307	8	6
α-helix	310-314	5
β-strand	319-324	6	7
β-strand	332-336	5	7
α-helix	338-340	3
β-strand	344	1	8
α-helix	345-346	2
β-strand	347-351	5	9
α-helix	352-354	3
α-helix	355-359	5
β-strand	362-372	11	9
β-strand	373	1	8
β-strand	378-383	6	10
β-strand	386-387	2	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	436-441	6	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin gamma-1 heavy chain	A, B	protein	223	Homo sapiens	P0DOX5 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5W5L_1 Immunoglobulin gamma-1 heavy chain (chains A, B)
TCPPCPAPEAAGASSVFLFPPKPKDTLMISRTPEVTCVVVDVSAEDPEVKFNWYVDGVEV
HNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPSSIEKTISKAKGQPR
EPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSF
FLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

Primary citation

Functional, Biophysical, and Structural Characterization of Human IgG1 and IgG4 Fc Variants with Ablated Immune Functionality. Tam, S.H., McCarthy, S.G., Armstrong, A.A. et al. Antibodies (Basel) (2017) 6. DOI 10.3390/antib6030012 · 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)
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…
8ECQ 2.0 Å, Bovine Fab 2G3

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