3CMP

Crystal structure of Siderocalin (NGAL, Lipocalin 2) K125A mutant complexed with Ferric Enterobactin

PDB DOI: https://doi.org/10.2210/pdb3CMP/pdb

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

Deposited: 2008-03-24 Released: 2009-05-12
Deposition Author(s): Clifton, M.C., Strong, R.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.304
R-Value Work: 0.248
R-Value Observed: 0.251

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: 70.16 kDa
Atom Count: 4,170
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): 2 Gene Names: LCN2, HNL, 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
EB4 Query on EB4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain U [auth C] MOL2 format, chain H [auth A] MOL2 format, chain U [auth C] mmCIF format, chain H [auth A] mmCIF format, chain U [auth C]	H [auth A], U [auth C]	N,N',N''-[(3S,7S,11S)-2,6,10-trioxo-1,5,9-trioxacyclododecane-3,7,11-triyl]tris(2,3-dihydroxybenzamide) C₃₀ H₂₇ N₃ O₁₅ SERBHKJMVBATSJ-BZSNNMDCSA-N		Interactions Focus chain H [auth A] Focus chain U [auth C] Interactions & Density Focus chain H [auth A] Focus chain U [auth C]
DBH Query on DBH Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	L [auth B], M [auth B]	2,3-DIHYDROXY-BENZOIC ACID C₇ H₆ O₄ GLDQAMYCGOIJDV-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain L [auth B] Focus chain M [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain T [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain T [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain T [auth C]	F [auth A], G [auth A], T [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain T [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain T [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain V [auth C] SDF format, chain W [auth C] MOL2 format, chain I [auth A] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] mmCIF format, chain I [auth A] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C]	I [auth A], V [auth C], W [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain I [auth A] Focus chain V [auth C] Focus chain W [auth C]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C]	D [auth A], J [auth B], N [auth C]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Focus chain N [auth C] Interactions & Density Focus chain D [auth A] Focus chain J [auth B] Focus chain N [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C]	E [auth A] K [auth B] O [auth C] P [auth C] Q [auth C] E [auth A], K [auth B], O [auth C], P [auth C], Q [auth C], R [auth C], S [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.304
R-Value Work: 0.248
R-Value Observed: 0.251
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.908	α = 90
b = 114.908	β = 90
c = 118.832	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-05-12

Deposition Author(s):

Clifton, M.C.

Strong, R.K.

Revision History (Full details and data files)

Version 1.0: 2009-05-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2019-02-27
Changes: Data collection, Database references
Version 1.3: 2021-10-20
Changes: Database references, Derived calculations
Version 1.4: 2023-08-30
Changes: Data collection, Refinement description
Version 1.5: 2024-11-13
Changes: Structure summary