3HWG | pdb_00003hwg

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 (Depositor), 0.260 (DCC)
R-Value Work:
0.242 (Depositor), 0.240 (DCC)
R-Value Observed:
0.245 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 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
Modeled 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 E [auth A] SDF format, chain S [auth B] SDF format, chain W [auth C] MOL2 format, chain E [auth A] MOL2 format, chain S [auth B] MOL2 format, chain W [auth C] mmCIF format, chain E [auth A] mmCIF format, chain S [auth B] mmCIF format, chain W [auth C]	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 P [auth A] SDF format, chain U [auth B] SDF format, chain Q [auth A] SDF format, chain O [auth A] SDF format, chain KA [auth C] SDF format, chain JA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain U [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain O [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain JA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain U [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain O [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain JA [auth C]	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 CA [auth C] SDF format, chain F [auth A] SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain T [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain DA [auth C] SDF format, chain BA [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain T [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain DA [auth C] MOL2 format, chain BA [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain T [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain DA [auth C] mmCIF format, chain BA [auth C]	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 R [auth B] SDF format, chain V [auth C] MOL2 format, chain D [auth A] MOL2 format, chain R [auth B] MOL2 format, chain V [auth C] mmCIF format, chain D [auth A] mmCIF format, chain R [auth B] mmCIF format, chain V [auth C]	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] mmCIF 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 K [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain L [auth A] SDF format, chain HA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain L [auth A] MOL2 format, chain HA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain L [auth A] mmCIF format, chain HA [auth C]	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 (Depositor), 0.260 (DCC)
R-Value Work: 0.242 (Depositor), 0.240 (DCC)
R-Value Observed: 0.245 (Depositor)

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
Version 1.5: 2024-10-30
Changes: Structure summary