4DMB | pdb_00004dmb

X-ray structure of human hepatitus C virus NS5A-transactivated protein 2 at the resolution 1.9A, Northeast Structural Genomics Consortium (NESG) Target HR6723

PDB DOI: https://doi.org/10.2210/pdb4DMB/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-02-07 Released: 2012-04-04
Deposition Author(s): Kuzin, A., Su, M., Seetharaman, J., Patel, P., Xiao, R., Ciccosanti, C., Lee, D., Everett, J.K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG), Mitochondrial Protein Partnership (MPP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.207 (Depositor), 0.203 (DCC)
R-Value Work:
0.175 (Depositor), 0.173 (DCC)
R-Value Observed:
0.177 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Northeast Structural Genomics Consortium Target HR6723

Kuzin, A., Su, M., Seetharaman, J., Patel, P., Xiao, R., Ciccosanti, C., Lee, D., Everett, J.K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 48.37 kDa
Atom Count: 3,354
Modeled Residue Count: 378
Deposited Residue Count: 408
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HD domain-containing protein 2	A, B	204	Homo sapiens	Mutation(s): 0 Gene Names: HDDC2, C6orf74, NS5ATP2, CGI-130 EC: 3.1.3.89
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z4H3 (Homo sapiens) Explore Q7Z4H3 Go to UniProtKB: Q7Z4H3
PHAROS: Q7Z4H3 GTEx: ENSG00000111906
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7Z4H3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A]	I [auth A], L [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Interactions & Density Focus chain I [auth A] Focus chain L [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A]	H [auth A], K [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth A] Focus chain K [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain E [auth A] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain C [auth A]	C [auth A], E [auth A], J [auth B]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain J [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain F [auth A] SDF format, chain D [auth A] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A]	D [auth A], F [auth A], N [auth B], O [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain N [auth B] Focus chain O [auth B]
UNL Query on UNL Download:Ideal Coordinates CCD File	M [auth B]	Unknown ligand JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.207 (Depositor), 0.203 (DCC)
R-Value Work: 0.175 (Depositor), 0.173 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.393	α = 90
b = 68.393	β = 90
c = 174.452	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AutoSol	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-04-04

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Mitochondrial Protein Partnership (MPP)

Revision History (Full details and data files)

Version 1.0: 2012-04-04
Type: Initial release
Version 1.1: 2012-04-11
Changes: Structure summary
Version 1.2: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary