8B50 | pdb_00008b50

Crystal structure of a Fab fragment in complex with L-hydroxycoumarylalanine

PDB DOI: https://doi.org/10.2210/pdb8B50/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-09-21 Released: 2023-10-04
Deposition Author(s): Meining, W., Eichinger, A., Skerra, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free:
0.221 (Depositor), 0.230 (DCC)
R-Value Work:
0.191 (Depositor), 0.200 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Preparation and characterization of monoclonal antibodies against a non natural amino acid carrying the 7-hydroxycoumarin side chain

Rubini, M., Meining, W., Eichinger, A., Mueller, M., Kramer, K., Skerra, A.

To be published.

Macromolecule Content

Total Structure Weight: 48.88 kDa
Atom Count: 3,645
Modeled Residue Count: 434
Deposited Residue Count: 446
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab fragment K12F9-22 - heavy chain	A [auth H]	227	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 fragment K12F9-22 - light chain	B [auth L]	219	Mus musculus	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
P0M (Subject of Investigation/LOI) Query on P0M Download Ideal Coordinates CCD File SDF format, chain C [auth H] MOL2 format, chain C [auth H] mmCIF format, chain C [auth H]	C [auth H]	(2~{S})-2-azanyl-3-(7-oxidanyl-2-oxidanylidene-chromen-4-yl)propanoic acid C₁₂ H₁₁ N O₅ UURZOUPNUFWGBS-VIFPVBQESA-N		Interactions Focus chain C [auth H] Interactions & Density Focus chain C [auth H]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth L] MOL2 format, chain D [auth L] mmCIF format, chain D [auth L]	D [auth L]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth L] Interactions & Density Focus chain D [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free: 0.221 (Depositor), 0.230 (DCC)
R-Value Work: 0.191 (Depositor), 0.200 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.914	α = 90
b = 70.914	β = 90
c = 91.043	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
BALBES	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-10-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-10-04
Type: Initial release
Version 1.1: 2024-11-13
Changes: Structure summary
Version 1.2: 2026-03-04
Changes: Refinement description

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.