6FPZ | pdb_00006fpz

Inter-alpha-inhibitor heavy chain 1, D298A

PDB DOI: https://doi.org/10.2210/pdb6FPZ/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli K-12
Mutation(s): Yes

Deposited: 2018-02-12 Released: 2019-02-27
Deposition Author(s): Briggs, D.C., Day, A.J.
Funding Organization(s): Arthritis Research UK

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.248 (Depositor), 0.249 (DCC)
R-Value Work:
0.217 (Depositor), 0.220 (DCC)
R-Value Observed:
0.218 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Inter-alpha-inhibitor heavy chain-1 has an integrin-like 3D structure mediating immune regulatory activities and matrix stabilization during ovulation

Briggs, D.C., Langford-Smith, A.W.W., Birchenough, H.L., Jowitt, T.A., Kielty, C.M., Enghild, J.J., Baldock, C., Milner, C.M., Day, A.J.

(2020) J Biological Chem

DOI: https://doi.org/10.1074/jbc.RA119.011916

Macromolecule Content

Total Structure Weight: 148.68 kDa
Atom Count: 10,106
Modeled Residue Count: 1,196
Deposited Residue Count: 1,320
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inter-alpha-trypsin inhibitor heavy chain H1	A, B	660	Homo sapiens	Mutation(s): 1 Gene Names: ITIH1, IGHEP1
UniProt & NIH Common Fund Data Resources
Find proteins for P19827 (Homo sapiens) Explore P19827 Go to UniProtKB: P19827
PHAROS: P19827 GTEx: ENSG00000055957
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19827
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.248 (Depositor), 0.249 (DCC)
R-Value Work: 0.217 (Depositor), 0.220 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 4₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.7	α = 90
b = 159.7	β = 90
c = 65.745	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-02-27

Deposition Author(s):

Briggs, D.C.

Day, A.J.

Funding Organization	Location	Grant Number
Arthritis Research UK	United Kingdom	19489

Revision History (Full details and data files)

Version 1.0: 2019-02-27
Type: Initial release
Version 1.1: 2019-07-17
Changes: Data collection, Database references
Version 1.2: 2020-03-18
Changes: Database references
Version 1.3: 2024-10-23
Changes: Data collection, Database references, Refinement description, Structure summary

6FPZ | pdb_00006fpz

Inter-alpha-inhibitor heavy chain 1, D298A

Literature

Inter-alpha-inhibitor heavy chain-1 has an integrin-like 3D structure mediating immune regulatory activities and matrix stabilization during ovulation

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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