3CDF: Immunoglobulin light chain

kI O18/O8 Y87H immunoglobulin light chain variable domain. Determined by X-ray diffraction at 1.53 Å resolution. Released 2 Sept 2008.

Method: X-ray diffraction
Resolution: 1.53 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,592
Mol. weight: 71.68 kDa
Released: 2 Sept 2008

Explore 3CDF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3CDF contains 23 α-helices and 66 β-strands across 6 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: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	1-3	3
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
β-strand	98	1	2
β-strand	102-106	5	2

Chain B: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	0-3	4
β-strand	4-7	4	3
β-strand	10-13	4	4
β-strand	19-25	7	3
β-strand	33-38	6	4
α-helix	43-44	2
β-strand	45-49	5	4
β-strand	53-54	2	4
α-helix	55	1
β-strand	62-65	4	3
β-strand	70-75	6	3
α-helix	80-82	3
β-strand	85-90	6	4
α-helix	96	1
β-strand	97-98	2	4
β-strand	102-106	5	4

Chain C: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	1-3	3
β-strand	4-7	4	5
β-strand	10-13	4	4
β-strand	19-25	7	5
β-strand	33-38	6	4
β-strand	45-49	5	4
β-strand	53-54	2	4
β-strand	62-67	6	5
β-strand	70-75	6	5
α-helix	80-82	3
β-strand	85-90	6	4
β-strand	98	1	4
β-strand	102-106	5	4

Chains D and F: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	0-3	4
β-strand	4-7	4	6
β-strand	10-13	4	7
β-strand	19-25	7	6
β-strand	33-38	6	7
α-helix	43-44	2
β-strand	45-49	5	7
β-strand	53-54	2	7
α-helix	55	1
β-strand	62-67	6	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	85-90	6	7
α-helix	96	1
β-strand	97-98	2	7
β-strand	102-106	5	7

Chain E: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	1-3	3
β-strand	4-7	4	8
β-strand	10-13	4	7
β-strand	19-25	7	8
β-strand	33-38	6	7
β-strand	45-49	5	7
β-strand	53-54	2	7
α-helix	55	1
β-strand	62-67	6	8
β-strand	70-75	6	8
α-helix	80-82	3
β-strand	85-90	6	7
β-strand	98	1	7
β-strand	102-106	5	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin light chain	A, B, C, D, E, F	protein	109	Homo sapiens	P01594 (AlphaFold model)

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

>3CDF_1 IMMUNOGLOBULIN LIGHT CHAIN (chains A, B, C, D, E, F)
STDIQMTQSPSSLSASVGDRVTITCQASQDISNYLNWYQQKPGKAPKLLIYDASNLETGV
PSRFSGSGSGTDFTFTISSLQPEDIATYHCQQYDNLPYTFGQGTKLEIK

Primary citation

Structural insights into the role of mutations in amyloidogenesis. Baden, E.M., Randles, E.G., Aboagye, A.K. et al. J Biol Chem (2008) 283:30950-30956. DOI 10.1074/jbc.M804822200 · PubMed

Other PDB entries of the same protein (UniProt P01594 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2Q20 1.3 Å, Structure of the germline Vk1 O18/O8 light chain variable domain homodimer
3CDC 1.53 Å, kI O18/O8 N34I/Y87H immunoglobulin light chain variable domain
1B0W 1.8 Å, Structural comparison of amyloidogenic light chain dimer in two crystal forms with…
1QP1 2.06 Å, Kappa variable light chain
1JV5 2.2 Å, Anti-blood group A Fv
3CDY 2.43 Å, AL-09 H87Y, immunoglobulin light chain variable domain
7CZQ 2.8 Å, S protein of SARS-CoV-2 in complex bound with P2B-1A10
4K07 2.83 Å, Crystal structure of the amyloid-forming immunoglobulin AL-103 cis-proline 95 mutant
7CZV 3.3 Å, S protein of SARS-CoV-2 in complex bound with P5A-1B6_3B
7CZU 3.4 Å, S protein of SARS-CoV-2 in complex bound with P5A-1B6_2B

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