1P7K: Anti-ssDNA antigen-binding fragment

Crystal structure of an anti-ssDNA antigen-binding fragment (Fab) bound to 4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid (HEPES). Determined by X-ray diffraction at 1.75 Å resolution. Released 11 May 2004.

Method: X-ray diffraction
Resolution: 1.75 Å
Organism: Mus musculus
Chains: 4
Atoms: 7,565
Mol. weight: 99.52 kDa
Released: 11 May 2004

Explore 1P7K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1P7K contains 34 α-helices and 87 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: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	10-13	4	12
β-strand	19-25	7	11
β-strand	33-38	6	12
β-strand	45-49	5	12
β-strand	53-54	2	12
α-helix	55	1
β-strand	62-67	6	11
β-strand	70-75	6	11
α-helix	80-82	3
β-strand	84-90	7	12
α-helix	96	1
β-strand	98	1	12
β-strand	102-106	5	12
β-strand	111	1	13
α-helix	112-113	2
β-strand	114-118	5	14
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	14
β-strand	140	1	13
β-strand	144-150	7	15
β-strand	153-155	3	15
β-strand	159-163	5	14
β-strand	173-182	10	14
α-helix	183-188	6
β-strand	191-198	8	15
β-strand	205-210	6	15

Chain B: 11 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	16
α-helix	7-9	3
β-strand	10-12	3	17
β-strand	18-25	8	16
α-helix	29-31	3
β-strand	34-39	6	17
β-strand	46-52	7	17
β-strand	56-59	4	17
α-helix	61-63	3
β-strand	64	1	16
β-strand	67-72	6	16
α-helix	73-75	3
β-strand	77-82	6	16
α-helix	84-86	3
β-strand	88-95	8	17
α-helix	96	1
β-strand	100C-103	4	17
β-strand	107-111	5	17
α-helix	114-116	3
β-strand	117	1	18
α-helix	118-119	2
β-strand	120-124	5	19
β-strand	135-145	11	19
β-strand	146	1	18
β-strand	151-154	4	20
α-helix	155-157	3
β-strand	159	1	20
β-strand	163-165	3	19
α-helix	166-168	3
β-strand	169-171	3	19
β-strand	174-184	11	19
β-strand	194-199	6	20
α-helix	200-202	3
β-strand	204-209	6	20

Chain H: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	6
α-helix	7-9	3
β-strand	10-12	3	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	34-39	6	7
β-strand	45-52	8	7
β-strand	56-59	4	7
α-helix	61-63	3
β-strand	67-72	6	6
α-helix	73-75	3
β-strand	77-82	6	6
α-helix	84-86	3
β-strand	88-95	8	7
α-helix	96	1
β-strand	100C-103	4	7
β-strand	107-111	5	7
β-strand	117	1	8
α-helix	118-119	2
β-strand	120-124	5	9
β-strand	135-145	11	9
β-strand	146	1	8
β-strand	151-154	4	10
α-helix	155-157	3
β-strand	159	1	10
β-strand	163-165	3	9
α-helix	166-168	3
β-strand	169-171	3	9
β-strand	174-184	11	9
β-strand	194-199	6	10
α-helix	200-202	3
β-strand	204-209	6	10

Chain L: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
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	62-66	5	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
α-helix	96	1
β-strand	98	1	2
β-strand	102-106	5	2
β-strand	111	1	3
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	153-155	3	5
β-strand	159-163	5	4
β-strand	173-182	10	4
α-helix	183-188	6
β-strand	191-197	7	5
β-strand	205-210	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
antibody light chain FAB	A, L	protein	214	Mus musculus	P01837 (AlphaFold model)
antibody heavy chain FAB	B, H	protein	224	Mus musculus	P01868 (AlphaFold model)

Sequence of entity 1 (A, L), FASTA

>1P7K_1 antibody light chain FAB (chains A, L)
ELQMTQSPASLSASVGETVTITCRASENIYSYLAWYQQKQGKSPQLLVYNAKTLAEGVPS
RFSGSGSGTQFSLKINSLQPEDFGSYYCQHHYGTPLTFGAGTKLELKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (B, H), FASTA

>1P7K_2 antibody heavy chain FAB (chains B, H)
QVKLLESGPELVKPGASVKMSCKASGYTFTSYVMHWVKQKPGQGLEWIGYINPYNDGTKY
NEKFKGKATLTSDKSSSTAYMELSSLTSEDSAVYYCVRGGYRPYYAMDYWGQGTSVTVSS
AKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSD
LYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCTS

Primary citation

Structure of an anti-DNA fab complexed with a non-DNA ligand provides insights into cross-reactivity and molecular mimicry. Schuermann, J.P., Henzl, M.T., Deutscher, S.L. et al. Proteins (2004) 57:269-278. DOI 10.1002/prot.20200 · PubMed

Other PDB entries of the same protein (UniProt P01837 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3D9A 1.2 Å, High Resolution Crystal Structure Structure of HyHel10 Fab Complexed to Hen Egg Lysozyme
1RUR 1.5 Å, Crystal Structure (I) of native Diels-Alder antibody 13G5 Fab at pH 8.0 with a data set…
2AJU 1.5 Å, Cyrstal structure of cocaine catalytic antibody 7A1 Fab'
2AJV 1.5 Å, Crystal Structure of Cocaine catalytic Antibody 7A1 Fab' in Complex with Cocaine
2W60 1.5 Å, Anti citrullinated Collagen type 2 antibody acc4
2W9D 1.57 Å, Structure of Fab fragment of the ICSM 18 - anti-Prp therapeutic antibody at 1.57 A…
3BKJ 1.59 Å, Crystal structure of Fab wo2 bound to the n terminal domain of amyloid beta peptide (1-16)
3BAE 1.59 Å, Crystal structure of Fab WO2 bound to the N terminal domain of Amyloid beta peptide (1-28)
2R1Y 1.6 Å, Crystal structure of S25-2 Fab in complex with Kdo analogues
2R2B 1.6 Å, Crystal structure of S25-2 Fab in complex with Kdo analogues
3BKM 1.6 Å, Structure of anti-amyloid-beta Fab WO2 (Form A, P212121)
3CFB 1.6 Å, High-resolution structure of blue fluorescent antibody EP2-19G2 in complex with stilbene…

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