4QAE

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), 0.213 (DCC)
R-Value Work:
0.166 (Depositor), 0.175 (DCC)
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
Modelled 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P81172
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P80188
Sequence Annotations Expand
Reference Sequence LOADING

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 P [auth A] SDF format, chain R [auth B] SDF format, chain T [auth D] SDF format, chain U [auth E] SDF format, chain V [auth E] SDF format, chain W [auth F] SDF format, chain X [auth F] SDF format, chain Y [auth F] MOL2 format, chain P [auth A] MOL2 format, chain R [auth B] MOL2 format, chain T [auth D] MOL2 format, chain U [auth E] MOL2 format, chain V [auth E] MOL2 format, chain W [auth F] MOL2 format, chain X [auth F] MOL2 format, chain Y [auth F] mmCIF format, chain P [auth A] mmCIF format, chain R [auth B] mmCIF format, chain T [auth D] mmCIF format, chain U [auth E] mmCIF format, chain V [auth E] mmCIF format, chain W [auth F] mmCIF format, chain X [auth F] mmCIF format, chain Y [auth F]	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 M [auth P] SDF format, chain N [auth S] SDF format, chain O [auth U] SDF format, chain Q [auth B] SDF format, chain S [auth D] MOL2 format, chain M [auth P] MOL2 format, chain N [auth S] MOL2 format, chain O [auth U] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth D] mmCIF format, chain M [auth P] mmCIF format, chain N [auth S] mmCIF format, chain O [auth U] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth D]	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), 0.213 (DCC)
R-Value Work: 0.166 (Depositor), 0.175 (DCC)
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

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

Prepare Data

Validate Data

Deposit Data

Help and Resources

4QAE

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

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2