8ZPU

Crystal structure of the anti-phosphorylated peptide C7 scFv antibody with peptide bound

PDB DOI: https://doi.org/10.2210/pdb8ZPU/pdb

Classification: IMMUNE SYSTEM
Organism(s): Oryctolagus cuniculus, Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2024-05-31 Released: 2024-12-11
Deposition Author(s): Caaveiro, J.M.M., Kawade, R., Tsumoto, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.345
R-Value Work: 0.304

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Origin of high binding affinity and selectivity of phosphorylated epitope-specific rabbit antibodies

Kasahara, K., Kawade, R., Nakakido, M., Matsunaga, R., Akiba, H., Entzminger, K.C., Maruyama, T., Okumura, S.C.J., Caaveiro, J.M.M., Kuroda, D., Tsumoto, K.

To be published.

Macromolecule Content

Total Structure Weight: 57.21 kDa
Atom Count: 3,648
Modelled Residue Count: 479
Deposited Residue Count: 538
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv	A, C [auth B]	257	Oryctolagus cuniculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PHE-PRO-GLN-PHE-SEP-TYR-SER	B [auth C], D	12	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	E [auth A] F [auth A] G [auth A] I [auth B] J [auth B] E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B]	H [auth A], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain H [auth A] Focus chain L [auth B]