3I0A

Crystal structure of Siderocalin (NGAL, Lipocalin 2) K134A mutant complexed with Ferric Enterobactin

PDB DOI: https://doi.org/10.2210/pdb3I0A/pdb

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

Deposited: 2009-06-24 Released: 2010-06-09
Deposition Author(s): Clifton, M.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.300
R-Value Work: 0.255
R-Value Observed: 0.257

Starting Model: experimental
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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: 69.88 kDa
Atom Count: 4,165
Modelled Residue Count: 514
Deposited Residue Count: 594
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	198	Homo sapiens	Mutation(s): 2 Gene Names: HNL, LCN2, NGAL
UniProt & NIH Common Fund Data Resources
Find proteins for P80188 (Homo sapiens) Explore P80188 Go to UniProtKB: 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
MCJ Query on MCJ Download Ideal Coordinates CCD File SDF format, chain N [auth C] MOL2 format, chain N [auth C]	N [auth C]	N-[(2,3-dihydroxyphenyl)carbonyl]-O-[(2S)-2-{[(2,3-dihydroxyphenyl)carbonyl]amino}-3-({N-[(2,3-dihydroxyphenyl)carbonyl]-L-seryl}oxy)propanoyl]-D-serine C₃₀ H₂₉ N₃ O₁₆ NTWRWGRCGVKQNS-KSZLIROESA-N		Interactions Focus chain N [auth C] Interactions & Density Focus chain N [auth C]
2DS Query on 2DS Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	N-[(2,3-dihydroxyphenyl)carbonyl]-O-[(2R)-2-{[(2,3-dihydroxyphenyl)carbonyl]amino}-3-hydroxypropanoyl]-L-serine C₂₀ H₂₀ N₂ O₁₁ KLXJDVFEFZPIMN-NEPJUHHUSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
3ET Query on 3ET Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	O-[(2R)-2-amino-3-(D-seryloxy)propanoyl]-N-[(2,3-dihydroxyphenyl)carbonyl]-L-serine C₁₆ H₂₁ N₃ O₁₀ ZXSIADNPWRCRTI-BBBLOLIVSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
DBH Query on DBH Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B]	I [auth B]	2,3-DIHYDROXY-BENZOIC ACID C₇ H₆ O₄ GLDQAMYCGOIJDV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth C] MOL2 format, chain D [auth A] MOL2 format, chain J [auth C]	D [auth A], J [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain J [auth C] Interactions & Density Focus chain D [auth A] Focus chain J [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C]	L [auth C], M [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth C] Focus chain M [auth C] Interactions & Density Focus chain L [auth C] Focus chain M [auth C]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C]	E [auth A], H [auth B], K [auth C]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C]