4QAE | pdb_00004qae

Crystal structure of an engineered lipocalin (Anticalin) in complex with human hepcidin

PDB DOI: https://doi.org/10.2210/pdb4QAE/pdb

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

Deposited: 2014-05-04 Released: 2015-05-06
Deposition Author(s): Giese, T., Skerra, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.206 (Depositor), 0.210 (DCC)
R-Value Work:
0.166 (Depositor)
R-Value Observed:
0.168 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure of a hepcidin-binding anticalin in complex with its peptide ligand

Giese, T., Skerra, A.

To be published.

Macromolecule Content

Total Structure Weight: 146.92 kDa
Atom Count: 9,938
Modeled Residue Count: 1,149
Deposited Residue Count: 1,278
Unique protein chains: 2

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepcidin	A [auth P] B [auth Q] C [auth R] D [auth S] E [auth T] A [auth P], B [auth Q], C [auth R], D [auth S], E [auth T], F [auth U]	25	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P81172 (Homo sapiens) Explore P81172 Go to UniProtKB: P81172
PHAROS: P81172 GTEx: ENSG00000105697
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P81172
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutrophil gelatinase-associated lipocalin	G [auth A] H [auth B] I [auth C] J [auth D] K [auth E] G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	188	Homo sapiens	Mutation(s): 26 Gene Names: engineered variant, 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain Y [auth F] SDF format, chain X [auth F] SDF format, chain W [auth F] SDF format, chain V [auth E] SDF format, chain U [auth E] SDF format, chain T [auth D] SDF format, chain R [auth B] SDF format, chain P [auth A] MOL2 format, chain Y [auth F] MOL2 format, chain X [auth F] MOL2 format, chain W [auth F] MOL2 format, chain V [auth E] MOL2 format, chain U [auth E] MOL2 format, chain T [auth D] MOL2 format, chain R [auth B] MOL2 format, chain P [auth A] mmCIF format, chain Y [auth F] mmCIF format, chain X [auth F] mmCIF format, chain W [auth F] mmCIF format, chain V [auth E] mmCIF format, chain U [auth E] mmCIF format, chain T [auth D] mmCIF format, chain R [auth B] mmCIF format, chain P [auth A]	P [auth A] R [auth B] T [auth D] U [auth E] V [auth E] P [auth A], R [auth B], T [auth D], U [auth E], V [auth E], W [auth F], X [auth F], Y [auth F]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain P [auth A] Focus chain R [auth B] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth F] Focus chain Y [auth F] Interactions & Density Focus chain P [auth A] Focus chain R [auth B] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth F] Focus chain Y [auth F]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain Q [auth B] SDF format, chain O [auth U] SDF format, chain N [auth S] SDF format, chain M [auth P] MOL2 format, chain S [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain O [auth U] MOL2 format, chain N [auth S] MOL2 format, chain M [auth P] mmCIF format, chain S [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain O [auth U] mmCIF format, chain N [auth S] mmCIF format, chain M [auth P]	M [auth P], N [auth S], O [auth U], Q [auth B], S [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth P] Focus chain N [auth S] Focus chain O [auth U] Focus chain Q [auth B] Focus chain S [auth D] Interactions & Density Focus chain M [auth P] Focus chain N [auth S] Focus chain O [auth U] Focus chain Q [auth B] Focus chain S [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.206 (Depositor), 0.210 (DCC)
R-Value Work: 0.166 (Depositor)
R-Value Observed: 0.168 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.894	α = 90
b = 126.894	β = 90
c = 156.707	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XDS	data reduction
Auto-Rickshaw	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-05-06

Deposition Author(s):

Giese, T.

Skerra, A.

Revision History (Full details and data files)

Version 1.0: 2015-05-06
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary

4QAE | pdb_00004qae

Crystal structure of an engineered lipocalin (Anticalin) in complex with human hepcidin

Literature

Structure of a hepcidin-binding anticalin in complex with its peptide ligand

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Biological Assembly 5

Biological Assembly 6

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2