8JOW: Antibody

Crystal structure of rabbit antibody with phosphorylated peptide bound. Determined by X-ray diffraction at 1.4 Å resolution. Released 12 Jun 2024.

Method: X-ray diffraction
Resolution: 1.4 Å
Organisms: Oryctolagus cuniculus, Homo sapiens
Chains: 4
Atoms: 4,072
Mol. weight: 53.59 kDa
Released: 12 Jun 2024

Explore 8JOW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8JOW contains 19 α-helices and 50 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, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	11-12	2	2
β-strand	18-24	7	1
α-helix	29-31	3
β-strand	34-39	6	3
β-strand	45-51	7	3
β-strand	57-59	3	3
α-helix	61-63	3
β-strand	67-72	6	1
β-strand	75-80	6	1
α-helix	85-87	3
β-strand	89-96	8	3
β-strand	99	1	4
β-strand	104-107	4	3
β-strand	111-113	3	3
β-strand	114-115	2	2
β-strand	136-138	3	5
α-helix	140	1
α-helix	142	1
β-strand	143-145	3	6
β-strand	151-157	7	5
α-helix	160-161	2
α-helix	162-164	3
β-strand	167-172	6	6
β-strand	179-183	5	6
β-strand	187-188	2	6
α-helix	189	1
β-strand	196-201	6	5
β-strand	204-209	6	5
α-helix	214-216	3
β-strand	218-225	8	6
α-helix	228-230	3
β-strand	234-236	3	6
β-strand	240-244	5	6

Chains B and D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	14	1	4

Chain C: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	11-12	2	8
β-strand	18-24	7	7
α-helix	29-31	3
β-strand	34-39	6	3
β-strand	45-51	7	3
β-strand	57-59	3	3
α-helix	61-63	3
β-strand	67-72	6	7
β-strand	75-80	6	7
α-helix	85-87	3
β-strand	89-96	8	3
β-strand	99	1	9
β-strand	104-107	4	3
β-strand	111-113	3	3
β-strand	114-115	2	8
β-strand	136-138	3	10
α-helix	140	1
α-helix	142	1
β-strand	143-145	3	11
β-strand	151-157	7	10
α-helix	160-161	2
α-helix	162-164	3
β-strand	167-172	6	11
β-strand	179-183	5	11
β-strand	187-188	2	11
α-helix	189	1
β-strand	196-201	6	10
β-strand	204-209	6	10
α-helix	214-216	3
β-strand	218-225	8	11
β-strand	234-236	3	11
β-strand	240-244	5	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antibody (scFv)	A, C	protein	246	Oryctolagus cuniculus
Arg-pro-his-phe-pro-gln-phe-sep-tyr-ser-ala-ser	B, D	protein	12	Homo sapiens	P31749 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>8JOW_1 Antibody (scFv) (chains A, C)
QEQLMESGGRLVTPGTPLTLTCTASGSDISTYSISWVRQAPGKGLEWIGHIGSSGTQYYA
SWAKGRFAISRASTTVDLRITGPTTEDTATYFCARRGVGYNLYYNMWGPGTLVTVSLGGG
GSGGGGSGGGGSAIDMTQTPSPVSAAVGGTVTINCQASQSVYNSKNLAWYQQKPGQPPKL
LIYDSSTLASGVSSRFRGSGSGTQFTLTISGVQSDDAATYYCQGEFSCSSGDCAGFGGGT
EVVVEG

Sequence of entity 2 (B, D), FASTA

>8JOW_2 ARG-PRO-HIS-PHE-PRO-GLN-PHE-SEP-TYR-SER-ALA-SER (chains B, D)
RPHFPQFSYSAS

Primary citation

Unveiling the structural mechanisms behind high affinity and selectivity in phosphorylated epitope-specific rabbit antibodies. Kasahara, K., Kawade, R., Nakakido, M. et al. J Biol Chem (2024) 300:107989-107989. DOI 10.1016/j.jbc.2024.107989 · PubMed

Other PDB entries of the same protein (UniProt P31749 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1UNQ 0.98 Å, High resolution crystal structure of the Pleckstrin Homology Domain Of Protein Kinase…
1UNR 1.25 Å, Crystal structure of the PH domain of PKB alpha in complex with a sulfate molecule
7MYX 1.39 Å, Crystal structure of the PH domain (R86A) of Akt1
1H10 1.4 Å, High resolution structure of the pleckstrin homology domain of protein kinase b/akt…
4GV1 1.49 Å, PKB alpha in complex with AZD5363
1UNP 1.65 Å, Crystal structure of the pleckstrin homology domain of PKB alpha
3QKL 1.9 Å, Spirochromane Akt Inhibitors
7NH5 1.9 Å, Co-Crystal Structure of Akt1 in Complex with Covalent-Allosteric Akt Inhibitor 6
8UW9 1.9 Å, Structure of AKT1(E17K) with compound 4
9TMV 1.9 Å, Akt1 mutant in complex with the 3-ethyl 1-methyl 1,4-substituted pyrazole containing…
2UVM 1.94 Å, Structure of PKBalpha PH domain in complex with a novel inositol headgroup surrogate,…
2UZR 1.94 Å, A transforming mutation in the pleckstrin homology domain of AKT1 in cancer (AKT1-PH_E17K)

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