7Q2O | pdb_00007q2o

Beta-lactoglobulin mutant FAW (I56F/L39A/M107W) in complex with desipramine (FAW-DSM#1)

PDB DOI: https://doi.org/10.2210/pdb7Q2O/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Bos taurus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-10-25 Released: 2022-05-11
Deposition Author(s): Loch, J.I., Barciszewski, J., Lewinski, K.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.221 (Depositor), 0.230 (DCC)
R-Value Work:
0.183 (Depositor), 0.192 (DCC)

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

New ligand-binding sites identified in the crystal structures of [beta]-lactoglobulin complexes with desipramine

Loch, J.I., Barciszewski, J., Sliwiak, J., Bonarek, P., Wrobel, P., Pokrywka, K., Shabalin, I.G., Minor, W., Jaskolski, M., Lewinski, K.

(2022) IUCrJ 9: 386-398

DOI: https://doi.org/10.1107/S2052252522004183

Macromolecule Content

Total Structure Weight: 37.88 kDa
Atom Count: 2,700
Modeled Residue Count: 308
Deposited Residue Count: 324
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactoglobulin	A [auth AAA], B [auth BBB]	162	Bos taurus	Mutation(s): 5 Gene Names: LGB
UniProt
Find proteins for P02754 (Bos taurus) Explore P02754 Go to UniProtKB: P02754
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02754
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DSM (Subject of Investigation/LOI) Query on DSM Download:Ideal Coordinates CCD File SDF format, chain D [auth AAA] SDF format, chain E [auth AAA] SDF format, chain G [auth AAA] SDF format, chain J [auth BBB] MOL2 format, chain D [auth AAA] MOL2 format, chain E [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain J [auth BBB] mmCIF format, chain D [auth AAA] mmCIF format, chain E [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain J [auth BBB]	D [auth AAA], E [auth AAA], G [auth AAA], J [auth BBB]	3-(10,11-DIHYDRO-5H-DIBENZO[B,F]AZEPIN-5-YL)-N-METHYLPROPAN-1-AMINE C₁₈ H₂₂ N₂ HCYAFALTSJYZDH-UHFFFAOYSA-N		Interactions Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain G [auth AAA] Focus chain J [auth BBB] Interactions & Density Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain G [auth AAA] Focus chain J [auth BBB]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth AAA] MOL2 format, chain C [auth AAA] mmCIF format, chain C [auth AAA]	C [auth AAA]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth AAA] Interactions & Density Focus chain C [auth AAA]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth AAA] SDF format, chain I [auth BBB] MOL2 format, chain H [auth AAA] MOL2 format, chain I [auth BBB] mmCIF format, chain H [auth AAA] mmCIF format, chain I [auth BBB]	H [auth AAA], I [auth BBB]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth AAA] Focus chain I [auth BBB] Interactions & Density Focus chain H [auth AAA] Focus chain I [auth BBB]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth AAA] MOL2 format, chain F [auth AAA] mmCIF format, chain F [auth AAA]	F [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth AAA] Interactions & Density Focus chain F [auth AAA]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.221 (Depositor), 0.230 (DCC)
R-Value Work: 0.183 (Depositor), 0.192 (DCC)

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.667	α = 90
b = 70.145	β = 90
c = 179.018	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-05-11

Deposition Author(s):

Loch, J.I.

Barciszewski, J.

Lewinski, K.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-05-11
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Derived calculations, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary

7Q2O | pdb_00007q2o

Beta-lactoglobulin mutant FAW (I56F/L39A/M107W) in complex with desipramine (FAW-DSM#1)

Literature

New ligand-binding sites identified in the crystal structures of [beta]-lactoglobulin complexes with desipramine

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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