3HWG

Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Fe-TrenCam-hopo2

PDB DOI: https://doi.org/10.2210/pdb3HWG/pdb

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

Deposited: 2009-06-17 Released: 2010-06-02
Deposition Author(s): Clifton, M.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.268
R-Value Work: 0.242
R-Value Observed: 0.245

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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: 71.63 kDa
Atom Count: 4,456
Modelled Residue Count: 516
Deposited Residue Count: 594
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	198	Homo sapiens	Mutation(s): 1 Gene Names: HNL, LCN2, 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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QED Query on QED Download Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain W [auth C] SDF format, chain E [auth A] MOL2 format, chain S [auth B] MOL2 format, chain W [auth C] MOL2 format, chain E [auth A]	E [auth A], S [auth B], W [auth C]	N,N'-{[(2-{[(2,3-dihydroxyphenyl)carbonyl]amino}ethyl)imino]diethane-2,1-diyl}bis(1-hydroxy-6-oxo-1,6-dihydropyridine-2 -carboxamide) C₂₅ H₂₈ N₆ O₉ UPWYYPIMZVCQNS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain S [auth B] Focus chain W [auth C] Interactions & Density Focus chain E [auth A] Focus chain S [auth B] Focus chain W [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain U [auth B] SDF format, chain KA [auth C] SDF format, chain O [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain U [auth B] MOL2 format, chain KA [auth C] MOL2 format, chain O [auth A]	IA [auth C] JA [auth C] KA [auth C] O [auth A] P [auth A] IA [auth C], JA [auth C], KA [auth C], O [auth A], P [auth A], Q [auth A], U [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain U [auth B] Interactions & Density Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain U [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain T [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain F [auth A] SDF format, chain H [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain T [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] F [auth A] AA [auth C], BA [auth C], CA [auth C], DA [auth C], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], T [auth B], Y [auth C], Z [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain T [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain T [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain V [auth C] SDF format, chain R [auth B] MOL2 format, chain D [auth A] MOL2 format, chain V [auth C] MOL2 format, chain R [auth B]	D [auth A], R [auth B], V [auth C]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain R [auth B] Focus chain V [auth C] Interactions & Density Focus chain D [auth A] Focus chain R [auth B] Focus chain V [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain X [auth C] MOL2 format, chain X [auth C]	X [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain X [auth C] Interactions & Density Focus chain X [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A]	EA [auth C] FA [auth C] GA [auth C] HA [auth C] K [auth A] EA [auth C], FA [auth C], GA [auth C], HA [auth C], K [auth A], L [auth A], M [auth A], N [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.268
R-Value Work: 0.242
R-Value Observed: 0.245
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.084	α = 90
b = 114.084	β = 90
c = 118.422	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-06-02

Deposition Author(s):

Clifton, M.C.

Revision History (Full details and data files)

Version 1.0: 2010-06-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2019-02-27
Changes: Data collection, Database references
Version 1.3: 2021-10-13
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2023-09-06
Changes: Data collection, Refinement description