1QLR: IgM kappa chain V-III

Crystal structure of the FAB fragment of a human monoclonal IgM cold agglutinin. Determined by X-ray diffraction at 2.83 Å resolution. Released 14 Sept 2000.

Method: X-ray diffraction
Resolution: 2.83 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 6,540
Mol. weight: 97.72 kDa
Released: 14 Sept 2000

Explore 1QLR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1QLR contains 24 α-helices and 86 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: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
α-helix	28-29	2
α-helix	30-31	3
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	85-90	6	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-106	5	2
β-strand	111	1	3
α-helix	112-113	2
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	159-163	5	4
α-helix	164-167	4
β-strand	173-182	10	4
α-helix	183-188	6
β-strand	191-197	7	5
β-strand	205-210	6	5

Chain B: 3 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	11-12	2	7
β-strand	18-25	8	6
β-strand	34-39	6	8
β-strand	46-51	6	8
β-strand	57-59	3	8
α-helix	64-66	3
β-strand	67-72	6	6
β-strand	77-82	6	6
α-helix	87-89	3
β-strand	91-97	7	8
β-strand	109-110	2	8
β-strand	114-116	3	8
β-strand	117-118	2	7
β-strand	124	1	9
β-strand	127-131	5	10
β-strand	145-153	9	10
β-strand	154	1	9
β-strand	159-164	6	11
β-strand	169	1	11
β-strand	173-175	3	10
β-strand	179-181	3	10
β-strand	184-192	9	10
β-strand	205-211	7	11
β-strand	217-222	6	11
α-helix	223-224	2

Chain C: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-13	4	13
β-strand	19-25	7	12
α-helix	28-29	2
α-helix	30-31	3
β-strand	33-38	6	13
β-strand	45-49	5	13
β-strand	53-54	2	13
α-helix	55	1
β-strand	62-67	6	12
β-strand	70-75	6	12
α-helix	80-82	3
β-strand	85-90	6	13
α-helix	96	1
β-strand	97-98	2	13
β-strand	102-106	5	13
β-strand	111	1	14
α-helix	112-113	2
β-strand	114-118	5	15
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	15
β-strand	140	1	14
β-strand	145-150	6	16
β-strand	159-163	5	15
β-strand	173-182	10	15
α-helix	183-188	6
β-strand	191-197	7	16
β-strand	205-210	6	16

Chain D: 2 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	17
β-strand	11-12	2	18
β-strand	18-25	8	17
β-strand	34-39	6	19
β-strand	46-51	6	19
β-strand	57-59	3	19
α-helix	64-66	3
β-strand	67-72	6	17
β-strand	77-82	6	17
α-helix	87-89	3
β-strand	91-97	7	19
β-strand	109-110	2	19
β-strand	114-116	3	19
β-strand	117-118	2	18
β-strand	124	1	20
β-strand	127-131	5	21
β-strand	145-153	9	21
β-strand	154	1	20
β-strand	159-163	5	22
β-strand	169	1	22
β-strand	173-175	3	21
β-strand	179-181	3	21
β-strand	184-192	9	21
β-strand	206-211	6	22
β-strand	217-221	5	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
IgM kappa chain V-III (kau cold agglutinin)	A, C	protein	215	HOMO SAPIENS	Q6PJF2 (AlphaFold model)
IgM FAB region IV-J(H4)-C (kau cold agglutinin)	B, D	protein	232	HOMO SAPIENS	P01871 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>1QLR_1 IGM KAPPA CHAIN V-III (KAU COLD AGGLUTININ) (chains A, C)
EIVLTQSPATLSLSPGERATLSCGASQSVSSNYLAWYQQKPGQAPRLLIYDASSRATGIP
DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPLTFGGGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B, D), FASTA

>1QLR_2 IGM FAB REGION IV-J(H4)-C (KAU COLD AGGLUTININ) (chains B, D)
EVQLQQWGAGLLKPSETLSLTCAVYGGSFSDYYWSWIRQPPGKGLEWIGEINHSGSTNYN
PSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARPPHDTSGHYWNYWGQGTLVTVSS
GSASAPTLFPLVSCENSPSDTSSVAVGCLAQDFLPDSITFSWKYKNNSDISSTRGFPSVL
RGGKYAATSQVLLPSKDVMQGTDEHVVCKVQHPNGNKEKNVPLPVIAELPPK

Primary citation

Three-dimensional structure of the Fab from a human IgM cold agglutinin. Cauerhff, A., Braden, B.C., Carvalho, J.G. et al. J Immunol (2000) 165:6422-6428. DOI 10.4049/jimmunol.165.11.6422 · PubMed

Other PDB entries of the same protein (UniProt Q6PJF2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3EO0 1.75 Å, Structure of the Transforming Growth Factor-Beta Neutralizing Antibody GC-1008
8QH0 1.87 Å, Crystal structure of the SARS-CoV-2 RBD with the antibody Cv2.3194
1DN0 2.28 Å, Structure of the FAB fragment from a human IgM cold agglutinin
2AGJ 2.6 Å, Crystal Structure of a glycosylated Fab from an IgM cryoglobulin with properties of a…
8QH1 2.65 Å, Crystal structure of the SARS-CoV-2 RBD from the Omicron BA4 variant with the antibody…
1U6A 2.81 Å, Crystal Structure of the Broadly Neutralizing Anti-HIV Fab F105
4YPG 3.0 Å, Structural Insights Into the Neutralization Properties of a Human Anti-Interferon…
3EO1 3.1 Å, Structure of the Fab Fragment of GC-1008 in Complex with Transforming Growth Factor-Beta 3
3B2V 3.3 Å, Crystal structure of the extracellular region of the epidermal growth factor receptor in…
6MYY 3.8 Å, Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 3 Fabs…
6UDK 3.9 Å, HIV-1 bNAb 1-55 in complex with modified BG505 SOSIP-based immunogen RC1 and 10-1074
6MZJ 4.8 Å, Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 2 Fabs…

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