4L7E

Three dimensional structure of mutant D78A of human HD domain-containing protein 2, Genomics Consortium (NESG) Target HR6723

PDB DOI: https://doi.org/10.2210/pdb4L7E/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2013-06-13 Released: 2013-07-24
Deposition Author(s): Kuzin, A., Su, M., Yakunin, A., Beloglazova, N., Seetharaman, J., Maglaqui, M., Xiao, R., Lee, D., Brown, G., Flick, R., Everett, J.K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.23 Å
R-Value Free: 0.215
R-Value Work: 0.174
R-Value Observed: 0.176

wwPDB Validation 3D Report Full Report

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

Literature

Northeast Structural Genomics Consortium Target HR6723

Kuzin, A., Su, M., Yakunin, A., Beloglazova, N., Seetharaman, J., Maglaqui, M., Xiao, R., Lee, D., Brown, G., Flick, R., Everett, J.K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

To be published.

Macromolecule Content

Total Structure Weight: 48.59 kDa
Atom Count: 3,263
Modelled Residue Count: 379
Deposited Residue Count: 408
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HD domain-containing protein 2	A, B	204	Homo sapiens	Mutation(s): 1 Gene Names: HDDC2, C6orf74, NS5ATP2, CGI-130
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7Z4H3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] J [auth B] D [auth A], E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], M [auth B], N [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth B] Focus chain N [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B]	C [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
UNL Query on UNL Download Ideal Coordinates CCD File	H [auth A], L [auth B]	Unknown ligand VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain H [auth A] Focus chain L [auth B]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET
SEP Query on SEP	A, B	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.23 Å
R-Value Free: 0.215
R-Value Work: 0.174
R-Value Observed: 0.176
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.762	α = 90
b = 68.886	β = 90
c = 106.154	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-07-24

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2013-07-24
Type: Initial release
Version 1.1: 2018-01-24
Changes: Database references, Structure summary
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-12-06
Changes: Data collection

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Help and Resources

4L7E

Three dimensional structure of mutant D78A of human HD domain-containing protein 2, Genomics Consortium (NESG) Target HR6723

Northeast Structural Genomics Consortium Target HR6723

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)