3K3L

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
R-Value Work: 0.260
R-Value Observed: 0.264

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: 3,940
Modelled Residue Count: 504
Deposited Residue Count: 534
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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]	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]	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 E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [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]	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 G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C]	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]	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]	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]