7FGJ

The cross-reaction complex structure with VQILNK peptide and the tau antibody's Fab domain.

PDB DOI: https://doi.org/10.2210/pdb7FGJ/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Homo sapiens
Mutation(s): No

Deposited: 2021-07-27 Released: 2022-07-27
Deposition Author(s): Tsuchida, T., Tsuchiya, T., Miyamoto, K., In, Y., Minoura, K., Taniguchi, T., Ishida, T., Tomoo, K.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.262 (Depositor), 0.270 (DCC)
R-Value Work:
0.196 (Depositor), 0.200 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The cross-reaction complex structure with VQILNK peptide and the antibody's Fab domain.

Tsuchida, T., Tsuchiya, T., Miyamoto, K., In, Y., Minoura, K., Taniguchi, T., Ishida, T., Tomoo, K.

To be published.

Macromolecule Content

Total Structure Weight: 49.06 kDa
Atom Count: 3,817
Modelled Residue Count: 439
Deposited Residue Count: 442
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab Heavy Chain	A [auth H]	219	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab Light Chain	B [auth L]	217	Mus musculus	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VQILNK	C	6	Homo sapiens	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain D [auth H] SDF format, chain E [auth H] SDF format, chain P [auth L] SDF format, chain Q [auth L] SDF format, chain R [auth L] MOL2 format, chain D [auth H] MOL2 format, chain E [auth H] MOL2 format, chain P [auth L] MOL2 format, chain Q [auth L] MOL2 format, chain R [auth L] mmCIF format, chain D [auth H] mmCIF format, chain E [auth H] mmCIF format, chain P [auth L] mmCIF format, chain Q [auth L] mmCIF format, chain R [auth L]	D [auth H], E [auth H], P [auth L], Q [auth L], R [auth L]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain D [auth H] Focus chain E [auth H] Focus chain P [auth L] Focus chain Q [auth L] Focus chain R [auth L] Interactions & Density Focus chain D [auth H] Focus chain E [auth H] Focus chain P [auth L] Focus chain Q [auth L] Focus chain R [auth L]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth H] SDF format, chain K [auth H] SDF format, chain L [auth H] SDF format, chain M [auth H] SDF format, chain N [auth H] SDF format, chain O [auth H] SDF format, chain V [auth L] SDF format, chain W [auth L] SDF format, chain X [auth L] MOL2 format, chain J [auth H] MOL2 format, chain K [auth H] MOL2 format, chain L [auth H] MOL2 format, chain M [auth H] MOL2 format, chain N [auth H] MOL2 format, chain O [auth H] MOL2 format, chain V [auth L] MOL2 format, chain W [auth L] MOL2 format, chain X [auth L] mmCIF format, chain J [auth H] mmCIF format, chain K [auth H] mmCIF format, chain L [auth H] mmCIF format, chain M [auth H] mmCIF format, chain N [auth H] mmCIF format, chain O [auth H] mmCIF format, chain V [auth L] mmCIF format, chain W [auth L] mmCIF format, chain X [auth L]	J [auth H] K [auth H] L [auth H] M [auth H] N [auth H] J [auth H], K [auth H], L [auth H], M [auth H], N [auth H], O [auth H], V [auth L], W [auth L], X [auth L]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth H] Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H] Focus chain N [auth H] Focus chain O [auth H] Focus chain V [auth L] Focus chain W [auth L] Focus chain X [auth L] Interactions & Density Focus chain J [auth H] Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H] Focus chain N [auth H] Focus chain O [auth H] Focus chain V [auth L] Focus chain W [auth L] Focus chain X [auth L]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth H] SDF format, chain G [auth H] SDF format, chain H SDF format, chain I [auth H] SDF format, chain S [auth L] SDF format, chain T [auth L] SDF format, chain U [auth L] MOL2 format, chain F [auth H] MOL2 format, chain G [auth H] MOL2 format, chain H MOL2 format, chain I [auth H] MOL2 format, chain S [auth L] MOL2 format, chain T [auth L] MOL2 format, chain U [auth L] mmCIF format, chain F [auth H] mmCIF format, chain G [auth H] mmCIF format, chain H mmCIF format, chain I [auth H] mmCIF format, chain S [auth L] mmCIF format, chain T [auth L] mmCIF format, chain U [auth L]	F [auth H] G [auth H] H I [auth H] S [auth L] F [auth H], G [auth H], H, I [auth H], S [auth L], T [auth L], U [auth L]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain I [auth H] Focus chain S [auth L] Focus chain T [auth L] Focus chain U [auth L] Interactions & Density Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain I [auth H] Focus chain S [auth L] Focus chain T [auth L] Focus chain U [auth L]