9FMB: Human IgD-Fc

Crystal structure of human IgD-Fc. Determined by X-ray diffraction at 3.0 Å resolution. Released 4 Dec 2024.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,302
Mol. weight: 109.64 kDa
Ligands: NAG
Released: 4 Dec 2024

Explore 9FMB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9FMB contains 17 α-helices and 76 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: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	297-302	6	1
α-helix	303-305	3
α-helix	306-311	6
β-strand	314-323	10	1
β-strand	330-335	6	2
β-strand	338	1	2
β-strand	344-346	3	1
β-strand	350-351	2	1
β-strand	357-366	10	1
α-helix	367-371	5
β-strand	376-382	7	2
β-strand	385-392	8	2
α-helix	398	1
β-strand	399	1	3
α-helix	400	1
β-strand	403-410	8	4
β-strand	419-428	10	4
β-strand	429	1	3
β-strand	433-439	7	5
β-strand	443-444	2	5
β-strand	447-453	7	4
β-strand	463-471	9	4
β-strand	481-488	8	5
β-strand	493-500	8	5

Chain B: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	297-302	6	6
α-helix	306-312	7
β-strand	314-323	10	6
α-helix	326-328	3
β-strand	330-335	6	7
β-strand	338	1	7
β-strand	344-346	3	6
β-strand	350-351	2	6
β-strand	357-366	10	6
α-helix	367-372	6
β-strand	376-381	6	7
β-strand	388-392	5	7
α-helix	399-401	3
β-strand	404-410	7	4
β-strand	419-428	10	4
β-strand	433-439	7	8
β-strand	442-444	3	8
β-strand	447-453	7	4
β-strand	463-471	9	4
β-strand	482-488	7	8
β-strand	493-496	4	8

Chain C: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	297-302	6	9
α-helix	303-305	3
α-helix	306-310	5
β-strand	314-323	10	9
β-strand	330-335	6	10
β-strand	338	1	10
α-helix	339-340	2
β-strand	344-346	3	9
β-strand	350-351	2	9
β-strand	357-366	10	9
α-helix	367-371	5
β-strand	376-381	6	10
β-strand	388-392	5	10
β-strand	399	1	11
α-helix	400-401	2
β-strand	403-406	4	12
β-strand	418-428	11	12
β-strand	429	1	11
β-strand	433-439	7	13
β-strand	442-444	3	13
β-strand	447	1	12
β-strand	450-453	4	12
β-strand	463-472	10	12
β-strand	481-488	8	13
β-strand	493-495	3	13
β-strand	498-500	3	13

Chain D: 3 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	297-302	6	14
α-helix	303-305	3
α-helix	306-312	7
β-strand	314-323	10	14
β-strand	330-335	6	15
β-strand	338	1	15
β-strand	344-346	3	14
β-strand	350-351	2	14
β-strand	357-366	10	14
α-helix	367-372	6
β-strand	376-381	6	15
β-strand	388-392	5	15
β-strand	399	1	16
β-strand	404-412	9	17
β-strand	418-428	11	17
β-strand	429	1	16
β-strand	433-439	7	18
β-strand	442-444	3	18
β-strand	447-450	4	17
β-strand	463-471	9	17
β-strand	482-488	7	18
β-strand	493-498	6	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 1 of Immunoglobulin heavy constant delta	A, B, C, D	protein	234	Homo sapiens	P01880 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>9FMB_1 Isoform 1 of Immunoglobulin heavy constant delta (chains A, B, C, D)
KTPECPSHTQPLGVYLLTPAVQDLWLRDKATFTCFVVGSDLKDAHLTWEVAGKVPTGGVE
EGLLERHSNGSQSQHSRLTLPRSLWNAGTSVTCTLNHPSLPPQRLMALREPAAQAPVKLS
LNLLASSDPPEAASWLLCEVSGFSPPNILLMWLEDQREVNTSGFAPARPPPQPRSTTFWA
WSVLRVPAPPSPQPATYTCVVSHEDSRTLLNASRSLEVSYVTDHGPMKHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Water and common crystallization additives (EDO, ACT, PEG) are not listed.

Primary citation

The Crystal Structure of Human IgD-Fc Reveals Unexpected Differences With Other Antibody Isotypes. Davies, A.M., Bui, T.T.T., Pacheco-Gomez, R. et al. Proteins (2025) 93:786-800. DOI 10.1002/prot.26771 · PubMed

Other PDB entries of the same protein (UniProt P01880 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1ZVO Semi-extended solution structure of human myeloma immunoglobulin D determined by…

Browse structure collections

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