8BF0 | pdb_00008bf0

Structure of a Fab portion from TKH2

PDB DOI: https://doi.org/10.2210/pdb8BF0/pdb

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

Deposited: 2022-10-23 Released: 2023-11-01
Deposition Author(s): Diskin, R., Borenstein-Katz, A.
Funding Organization(s): Israel Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.202 (Depositor), 0.203 (DCC)
R-Value Work:
0.168 (Depositor), 0.168 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Structure of a Fab portion from TKH2

Diskin, R., Borenstein-Katz, A.

To be published.

Macromolecule Content

Total Structure Weight: 46.57 kDa
Atom Count: 3,517
Modeled Residue Count: 424
Deposited Residue Count: 429
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-dectin-1 15E2 light chain	A [auth L]	213	Mus musculus	Mutation(s): 0

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-lox-1 15C4 heavy chain	B [auth H]	216	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain D [auth L] SDF format, chain C [auth L] MOL2 format, chain D [auth L] MOL2 format, chain C [auth L] mmCIF format, chain D [auth L] mmCIF format, chain C [auth L]	C [auth L], D [auth L]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain C [auth L] Focus chain D [auth L] Interactions & Density Focus chain C [auth L] Focus chain D [auth L]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth L] SDF format, chain E [auth L] MOL2 format, chain F [auth L] MOL2 format, chain E [auth L] mmCIF format, chain F [auth L] mmCIF format, chain E [auth L]	E [auth L], F [auth L]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth L] Focus chain F [auth L] Interactions & Density Focus chain E [auth L] Focus chain F [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.202 (Depositor), 0.203 (DCC)
R-Value Work: 0.168 (Depositor), 0.168 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.259	α = 90
b = 65.111	β = 104.55
c = 56.713	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-11-01

Deposition Author(s):

Borenstein-Katz, A.

Funding Organization	Location	Grant Number
Israel Science Foundation	Israel	209/20

Revision History (Full details and data files)

Version 1.0: 2023-11-01
Type: Initial release
Version 1.1: 2024-11-20
Changes: Structure summary
Version 1.2: 2026-03-04
Changes: Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.