3HLT - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF HUMAN HALOACID DEHALOGENASE-LIKE HYDROLASE DOMAIN CONTAINING 2 (HDHD2)

Authors :   E. Ugochukwu, N. Shafqat, W. W. Yue, R. Cocking, J. E. Bray, J. R. C. Muniz T. Krojer, F. Von Delft, C. Bountra, C. H. Arrowsmith, J. Weigelt, A. E U. Oppermann, Structural Genomics Consortium (Sgc)

Date :   28 May 09 (Deposition) - 07 Jul 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: C  (1x)
Biol. Unit 3: C  (2x)
Biol. Unit 4: A  (2x)

Keywords :   Hdhd2, Haloacid Dehalogenase-Like Hydrolase Domain Containing 2, Structural Genomics, Structural Genomics Consortium, Sgc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Ugochukwu, N. Shafqat, W. W. Yue, R. Cocking, J. E. Bray, J. R. C. Muniz, T. Krojer, F. Von Delft, C. Bountra, C. H. Arrowsmith, J. Weigelt, A. Edwards, U. Oppermann, Structural Genomics Consortium (Sgc)
The Crystal Structure Of Human Haloacid Dehalogenase-Like Hydrolase Domain Containing 2 (Hdhd2)
To Be Published
PubMed: search

Molecule 1 - HDHD2
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC-CTHF
	Expression System Strain	:	BL21(DE3)-R3-PRARE2
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	HDHD2
	Gene	:	HDHD2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HALOACID DEHALOGENASE-LIKE HYDROLASE DOMAIN-CONTAINING PROTEIN 2

		1	2
Asymmetric Unit	:	A	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		C
Biological Unit 3 (2x)	:		C
Biological Unit 4 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	NA	2	Ligand/Ion	SODIUM ION
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	NA	-1	Ligand/Ion	SODIUM ION
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	NA	-1	Ligand/Ion	SODIUM ION
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	NA	-1	Ligand/Ion	SODIUM ION
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 4 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	NA	-1	Ligand/Ion	SODIUM ION
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:48 , THR A:49 , LYS A:50 , LEU A:117 , HIS A:144 , HOH A:302	BINDING SITE FOR RESIDUE SO4 A 267
2	AC2	SOFTWARE	GLY A:191	BINDING SITE FOR RESIDUE CL A 268
3	AC3	SOFTWARE	ASP A:13 , SER A:15 , ASP A:204 , ASP A:209 , HOH A:307 , HOH A:314	BINDING SITE FOR RESIDUE NA A 269
4	AC4	SOFTWARE	THR C:48 , THR C:49 , LYS C:50 , LEU C:117 , HIS C:144	BINDING SITE FOR RESIDUE SO4 C 267
5	AC5	SOFTWARE	GLY C:191 , THR C:192 , GLY C:193	BINDING SITE FOR RESIDUE CL C 268
6	AC6	SOFTWARE	ASP C:13 , SER C:15 , ASP C:204	BINDING SITE FOR RESIDUE NA C 269

(no "SS Bond" information available for 3HLT)

Asymmetric Unit

No.	Residues
1	Ile A:20	-	Glu A:21
2	Lys A:179	-	Pro A:180
3	Asn A:237	-	Pro A:238
4	Lys C:179	-	Pro C:180
5	Asn C:237	-	Pro C:238

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_032289	R	85	Q	HDHD2_HUMAN	Polymorphism	7230131	A/C	R	85	Q

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_032289	R	85	Q	HDHD2_HUMAN	Polymorphism	7230131	A	R	85	Q

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_032289	R	85	Q	HDHD2_HUMAN	Polymorphism	7230131	C	R	85	Q

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_032289	R	85	Q	HDHD2_HUMAN	Polymorphism	7230131	C	R	85	Q

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 4 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_032289	R	85	Q	HDHD2_HUMAN	Polymorphism	7230131	A	R	85	Q

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 3HLT)

(no "Exon" information available for 3HLT)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:256
 aligned with HDHD2_HUMAN | Q9H0R4 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:256
                                                                                                                                                                                                                                                                                        259 
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254    | 
          HDHD2_HUMAN     5 RALKAVLVDLSGTLHIEDAAVPGAQEALKRLRGASVIIRFVTNTTKESKQDLLERLRKLEFDISEDEIFTSLTAARSLLERKQVRPMLLVDDRALPDFKGIQTSDPNAVVMGLAPEHFHYQILNQAFRLLLDGAPLIAIHKARYYKRKDGLALGPGPFVTALEYATDTKATVVGKPEKTFFLEALRGTGCEPEEAVMIGDDCRDDVGGAQDVGMLGILVKTGKYRASDEEKINPPPYLTCESFPHAVDHILQHLL-   -
               SCOP domains d3hlta_ A: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains 3hltA01 A:5-88,A:178-260  [code=3.40.50.1000, no name defined]                      3hltA02 A:89-177 4-nitrophenylphosphatase; domain 2                                      3hltA01 A:5-88,A:178-260  [code=3.40.50.1000, no name defined]                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.............hhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhh....hhh.eeehhhhhhhhhhhhh..eeee.hhhhhhhhh........eeee.......hhhhhhhhhhhhhh...eee.....eeee..eeee.hhhhhhhhhhhhh...ee....hhhhhhhhhh....hhh.eeeee.....hhhhhhh...eeeee.......hhhhhh.....eee.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------Q------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hlt A   5 RALKAVLVDLSGTLHIEDAAVPGAQEALKRLRGASVIIRFVTNTTKESKQDLLERLRKLEFDISEDEIFTSLTAARSLLERKQVRPMLLVDDRALPDFKGIQTSDPNAVVMGLAPEHFHYQILNQAFRLLLDGAPLIAIHKARYYKRKDGLALGPGPFVTALEYATDTKATVVGKPEKTFFLEALRGTGCEPEEAVMIGDDCRDDVGGAQDVGMLGILVKTGKYRASDEEKINPPPYLTCESFPHAVDHILQHLLA 260
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254

Chain C from PDB  Type:PROTEIN  Length:243
 aligned with HDHD2_HUMAN | Q9H0R4 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:254
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255    
          HDHD2_HUMAN     6 ALKAVLVDLSGTLHIEDAAVPGAQEALKRLRGASVIIRFVTNTTKESKQDLLERLRKLEFDISEDEIFTSLTAARSLLERKQVRPMLLVDDRALPDFKGIQTSDPNAVVMGLAPEHFHYQILNQAFRLLLDGAPLIAIHKARYYKRKDGLALGPGPFVTALEYATDTKATVVGKPEKTFFLEALRGTGCEPEEAVMIGDDCRDDVGGAQDVGMLGILVKTGKYRASDEEKINPPPYLTCESFPHAVDHILQHLL 259
               SCOP domains d3hltc_ C: a       utomated ma    tches                                                                                                                                                                                                                        SCOP domains
               CATH domains 3hltC01 C:6-       88,C:178-25    9  [code=3.40.50.1000, no name defined]          3hltC02 C:89-177 4-nitrophenylphosphatase; domain 2                                      3hltC01 C:6-88,C:178-259  [code=3.40.50.1000, no name defined]                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....-------..hhhhhhhhh----.eeeeee.....hhhhhhhhhhhh....hhh.eeehhhhhhhhhhhhh..eeee.hhhhhhhhh........eeee.......hhhhhhhhhhhhh....eee.....eeee..eeee.hhhhhhhhhhhhh...ee....hhhhhhhhh.....hhh.eeeee.....hhhhhhh...eeeee.......hhhhhh.....eee.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------Q------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hlt C   6 ALKAVLVDLSGT-------VPGAQEALKRL----VIIRFVTNTTKESKQDLLERLRKLEFDISEDEIFTSLTAARSLLERKQVRPMLLVDDRALPDFKGIQTSDPNAVVMGLAPEHFHYQILNQAFRLLLDGAPLIAIHKARYYKRKDGLALGPGPFVTALEYATDTKATVVGKPEKTFFLEALRGTGCEPEEAVMIGDDCRDDVGGAQDVGMLGILVKTGKYRASDEEKINPPPYLTCESFPHAVDHILQHLL 259
                                    15 |      25        35    |   45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255    
                                      17      25        35   40

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: HAD-like (349)

Superfamily: HAD-like (349)

Family: automated matches (99)

Protein domain: automated matches (99)

Human (Homo sapiens) [TaxId: 9606] (9)

1a	d3hlta_	A:
1b	d3hltc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1000, no name defined] (211)

Human (Homo sapiens) (42)

1a	3hltA01	A:5-88,A:178-260
1b	3hltC01	C:6-88,C:178-259

Homologous Superfamily: 4-nitrophenylphosphatase; domain 2 (12)

Human (Homo sapiens) (2)

2a	3hltA02	A:89-177
2b	3hltC02	C:89-177

(no "Pfam Domain" information available for 3HLT)

Asymmetric Unit(hide GO term definitions)

Chain A,C (HDHD2_HUMAN | Q9H0R4)

molecular function
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016791	phosphatase activity	Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0008150	biological_process	Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
cellular component
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

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	Cis Peptide Bonds
		Asn A:237 - Pro A:238	[ RasMol ]
		Asn C:237 - Pro C:238	[ RasMol ]
		Ile A:20 - Glu A:21	[ RasMol ]
		Lys A:179 - Pro A:180	[ RasMol ]
		Lys C:179 - Pro C:180	[ RasMol ]

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2ho4	CRYSTAL STRUCTURE OF PROTEIN FROM MOUSE MM.236127

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

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