3TF6

Crystal structure of Neutrophil gelatinase-associated lipocalin (C87S mutant) in complex with Europium and the siderophore analog tren(cam)(1,2-hopo)2

PDB DOI: https://doi.org/10.2210/pdb3TF6/pdb

Classification: ANTIMICROBIAL PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2011-08-15 Released: 2011-09-07
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.216
R-Value Work: 0.191
R-Value Observed: 0.194

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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: 63.59 kDa
Atom Count: 4,300
Modelled Residue Count: 520
Deposited Residue Count: 537
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutrophil gelatinase-associated lipocalin	A, B, C	179	Homo sapiens	Mutation(s): 1 Gene Names: LCN2, HNL, NGAL
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P80188
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DBH Query on DBH Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain O [auth C] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain O [auth C]	F [auth A], J [auth B], O [auth C]	2,3-DIHYDROXY-BENZOIC ACID C₇ H₆ O₄ GLDQAMYCGOIJDV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain O [auth C] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain O [auth C]
EU Query on EU Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain N [auth C] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain N [auth C] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain N [auth C]	E [auth A], I [auth B], N [auth C]	EUROPIUM ION Eu MGVUQZZTJGLWJV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain P [auth C] SDF format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C] MOL2 format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain P [auth C] mmCIF format, chain G [auth A]	G [auth A], K [auth B], P [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain P [auth C] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain P [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain R [auth C] SDF format, chain D [auth A] SDF format, chain Q [auth C] MOL2 format, chain M [auth C] MOL2 format, chain R [auth C] MOL2 format, chain D [auth A] MOL2 format, chain Q [auth C] mmCIF format, chain M [auth C] mmCIF format, chain R [auth C] mmCIF format, chain D [auth A] mmCIF format, chain Q [auth C]	D [auth A], M [auth C], Q [auth C], R [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain M [auth C] Focus chain Q [auth C] Focus chain R [auth C] Interactions & Density Focus chain D [auth A] Focus chain M [auth C] Focus chain Q [auth C] Focus chain R [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain L [auth B] SDF format, chain U [auth C] MOL2 format, chain H [auth A] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain L [auth B] MOL2 format, chain U [auth C] mmCIF format, chain H [auth A] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain L [auth B] mmCIF format, chain U [auth C]	H [auth A], L [auth B], S [auth C], T [auth C], U [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
DBH	PDBBind: 3TF6	Kd: 400 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.216
R-Value Work: 0.191
R-Value Observed: 0.194
Space Group: P 4₁ 2₁ 2
Diffraction Data: https://doi.org/10.18430/M33TF6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.09	α = 90
b = 114.09	β = 90
c = 118.19	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-09-07

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2011-09-07
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: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary