6N9T: Immunoglobulin G1 FC

Structure of a peptide-based photo-affinity cross-linker with Herceptin Fc. Determined by X-ray diffraction at 2.58 Å resolution. Released 16 Jan 2019.

Method: X-ray diffraction
Resolution: 2.58 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 3,894
Mol. weight: 56.37 kDa
Released: 16 Jan 2019

Explore 6N9T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6N9T contains 22 α-helices and 44 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: 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	310-314	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	386-388	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	414-419	6
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	7
α-helix	244-246	3
α-helix	247-251	5
β-strand	258-267	10	7
β-strand	274-279	6	8
β-strand	282-284	3	8
β-strand	288-289	2	7
α-helix	290-292	3
β-strand	293-294	2	7
β-strand	299-307	9	7
α-helix	310-314	5
β-strand	319-324	6	8
β-strand	332-336	5	8
α-helix	339-340	2
β-strand	344	1	9
α-helix	345-346	2
β-strand	347-351	5	10
α-helix	352-354	3
α-helix	355-359	5
β-strand	362-372	11	10
β-strand	373	1	9
β-strand	378-383	6	11
β-strand	386-388	3	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	436-441	6	11

Chains E and F: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	6
β-strand	8-12	5	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin G1 FC	A, B	protein	224	Homo sapiens	Q6MZV7 (AlphaFold model)
Photo-affinity peptide	E, F	protein	13	synthetic construct

Sequence of entity 1 (A, B), FASTA

>6N9T_1 Immunoglobulin G1 FC (chains A, B)
THTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGV
EVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQ
PREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDG
SFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPG

Sequence of entity 2 (E, F), FASTA

>6N9T_2 Photo-affinity peptide (chains E, F)
DCAWHLGELFWCT

Primary citation

Development, Optimization, and Structural Characterization of an Efficient Peptide-Based Photoaffinity Cross-Linking Reaction for Generation of Homogeneous Conjugates from Wild-Type Antibodies. Vance, N., Zacharias, N., Ultsch, M. et al. Bioconjug Chem (2019) 30:148-160. DOI 10.1021/acs.bioconjchem.8b00809 · 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
5NSC 2.3 Å, Fc DEKK heterodimer 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…
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

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