3K3L | pdb_00003k3l

Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with apo Enterobactin

PDB DOI: https://doi.org/10.2210/pdb3K3L/pdb

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

Deposited: 2009-10-02 Released: 2010-08-18
Deposition Author(s): Clifton, M.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free:
0.307 (Depositor), 0.303 (DCC)
R-Value Work:
0.260 (Depositor), 0.261 (DCC)
R-Value Observed:
0.264 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3K3L

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: 63.59 kDa
Atom Count: 3,940
Modeled Residue Count: 504
Deposited Residue Count: 534
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutrophil gelatinase-associated lipocalin	A, B, C	178	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80188
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MCK Query on MCK Download:Ideal Coordinates CCD File SDF format, chain K [auth C] MOL2 format, chain K [auth C] mmCIF format, chain K [auth C]	K [auth C]	N-[(2,3-dihydroxyphenyl)carbonyl]-O-[(2S)-2-{[(2,3-dihydroxyphenyl)carbonyl]amino}-3-(L-seryloxy)propanoyl]-L-serine C₂₃ H₂₅ N₃ O₁₃ AVZOYWMPRGKOPV-IHRRRGAJSA-N		Interactions Focus chain K [auth C] Interactions & Density Focus chain K [auth C]
DBS Query on DBS Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	2-(2,3-DIHYDROXY-BENZOYLAMINO)-3-HYDROXY-PROPIONIC ACID C₁₀ H₁₁ N O₆ VDTYHTVHFIIEIL-LURJTMIESA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
DBH Query on DBH Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A]	2,3-DIHYDROXY-BENZOIC ACID C₇ H₆ O₄ GLDQAMYCGOIJDV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth C] SDF format, chain N [auth C] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain M [auth C] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth C] MOL2 format, chain N [auth C] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain M [auth C] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth C] mmCIF format, chain N [auth C] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain M [auth C] mmCIF format, chain G [auth A]	G [auth A] H [auth A] L [auth C] M [auth C] N [auth C] G [auth A], H [auth A], L [auth C], M [auth C], N [auth C], O [auth C], P [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain R [auth C] MOL2 format, chain R [auth C] mmCIF format, chain R [auth C]	R [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain R [auth C] Interactions & Density Focus chain R [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain Q [auth C] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth C] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth C]	I [auth A], Q [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain Q [auth C] Interactions & Density Focus chain I [auth A] Focus chain Q [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free: 0.307 (Depositor), 0.303 (DCC)
R-Value Work: 0.260 (Depositor), 0.261 (DCC)
R-Value Observed: 0.264 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.2	α = 90
b = 114.2	β = 90
c = 119.3	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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-08-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-08-18
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
Version 1.4: 2024-10-09
Changes: Data collection, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.