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)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 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

Find similar proteins by:

(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

Find similar proteins by:

(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

View Full Validation Report

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

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.