3TZS | pdb_00003tzs

Crystal structure of Neutrophil gelatinase-associated lipocalin NGAL (C87S mutant) in complex with fragment 1026, phenylurea

PDB DOI: https://doi.org/10.2210/pdb3TZS/pdb

Classification: APOPTOSIS
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2011-09-27 Released: 2011-10-12
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.225 (Depositor), 0.224 (DCC)
R-Value Work:
0.187 (Depositor), 0.186 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Parsing the functional specificity of Siderocalin / Lipocalin 2 / NGAL for siderophores and related small-molecule ligands

Clifton, M.C., Rupert, P.B., Hoette, T.M., Raymond, K.N., Abergel, R.J., Strong, R.K.

To be published.

Macromolecule Content

Total Structure Weight: 64.81 kDa
Atom Count: 4,356
Modeled Residue Count: 520
Deposited Residue Count: 549
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutrophil gelatinase-associated lipocalin	A, B, C	183	Homo sapiens	Mutation(s): 1 Gene Names: HNL, LCN2, NGAL, Oncogene 24p3
UniProt & NIH Common Fund Data Resources
Find proteins for P80188 (Homo sapiens) Explore P80188 Go to UniProtKB: P80188
PHAROS: P80188 GTEx: ENSG00000148346
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80188
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PHU Query on PHU Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain S [auth C] MOL2 format, chain D [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain S [auth C] mmCIF format, chain D [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain S [auth C]	D [auth A], H [auth A], J [auth B], N [auth C], S [auth C]	1-phenylurea C₇ H₈ N₂ O LUBJCRLGQSPQNN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain S [auth C] Interactions & Density Focus chain D [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain S [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain R [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain R [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C]	E [auth A] G [auth A] K [auth B] M [auth B] O [auth C] E [auth A], G [auth A], K [auth B], M [auth B], O [auth C], R [auth C], T [auth C], U [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain R [auth C] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain R [auth C] Focus chain T [auth C] Focus chain U [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain P [auth C] MOL2 format, chain I [auth A] MOL2 format, chain P [auth C] mmCIF format, chain I [auth A] mmCIF format, chain P [auth C]	I [auth A], P [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain P [auth C] Interactions & Density Focus chain I [auth A] Focus chain P [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain Q [auth C] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth C]	F [auth A], L [auth B], Q [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain Q [auth C] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain Q [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.225 (Depositor), 0.224 (DCC)
R-Value Work: 0.187 (Depositor), 0.186 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.35	α = 90
b = 115.35	β = 90
c = 119.89	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-10-12

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2011-10-12
Type: Initial release
Version 1.1: 2013-10-09
Changes: Database references
Version 1.2: 2019-02-13
Changes: Data collection, Database references
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-09
Changes: Structure summary