4KNW - 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)

Title :   THE CRYSTAL STRUCTURE OF HUMAN HDHD4 IN COMPLEX WITH MAGNESIUM AND THE PHOSPHATE MIMETIC VANADATE

Authors :   H. E. Klei

Date :   10 May 13 (Deposition) - 26 Jun 13 (Release) - 10 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   N-Acetylneuraminate, Neu5Ac-9-Phosphate, Carbohydrate Metabolism, N- Acetylneuraminic Acid Phosphatase, Nanp, Hdhd4, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. H. Kim, K. L. Constantine, G. J. Duke, V. Goldfarb, J. T. Hunt, S. Johnson, K. Kish, H. E. Klei, P. A. Mcdonnell, W. J. Metzler, L. Mueller, M. A. Poss, C. R. Fairchild, R. S. Bhide
Design, Synthesis, Functional And Structural Characterization Of An Inhibitor Of N-Acetylneuraminate-9-Phosphate Phosphatase: Observation Of Extensive Dynamics In An Enzyme/Inhibitor Complex.
Bioorg. Med. Chem. Lett. V. 23 4107 2013
PubMed-ID: 23747226 | Reference-DOI: 10.1016/J.BMCL.2013.05.052

Molecule 1 - N-ACYLNEURAMINATE-9-PHOSPHATASE
	Chains	:	A, B, C
	EC Number	:	3.1.3.29
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	C20ORF147, HDHD4, NANP
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HALOACID DEHALOGENASE-LIKE HYDROLASE DOMAIN-CONTAINING PROTEIN 4, NEU5AC-9-PASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	MG	3	Ligand/Ion	MAGNESIUM ION
2	VO4	3	Ligand/Ion	VANADATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	VO4	1	Ligand/Ion	VANADATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	VO4	1	Ligand/Ion	VANADATE ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	VO4	1	Ligand/Ion	VANADATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:14 , LEU A:15 , ASP A:16 , THR A:133 , ASN A:134 , LYS A:166 , MG A:302	BINDING SITE FOR RESIDUE VO4 A 301
2	AC2	SOFTWARE	ASP A:14 , ASP A:16 , ASP A:191 , VO4 A:301	BINDING SITE FOR RESIDUE MG A 302
3	AC3	SOFTWARE	ASP B:14 , LEU B:15 , ASP B:16 , THR B:133 , ASN B:134 , LYS B:166 , ASP B:196 , MG B:302	BINDING SITE FOR RESIDUE VO4 B 301
4	AC4	SOFTWARE	ASP B:14 , ASP B:16 , ASP B:191 , THR B:192 , VO4 B:301	BINDING SITE FOR RESIDUE MG B 302
5	AC5	SOFTWARE	ASP C:14 , LEU C:15 , ASP C:16 , THR C:133 , ASN C:134 , LYS C:166 , ASP C:196 , MG C:302	BINDING SITE FOR RESIDUE VO4 C 301
6	AC6	SOFTWARE	ASP C:14 , ASP C:16 , ASP C:191 , VO4 C:301	BINDING SITE FOR RESIDUE MG C 302

(no "SS Bond" information available for 4KNW)

Asymmetric Unit

No.	Residues
1	His A:64	-	Pro A:65
2	Thr A:68	-	Cys A:69
3	Lys A:166	-	Pro A:167
4	Glu B:61	-	Cys B:62
5	His B:64	-	Pro B:65
6	Lys B:166	-	Pro B:167
7	Ser C:6	-	Arg C:7
8	Phe C:63	-	His C:64
9	Lys C:166	-	Pro C:167
10	Ile C:242	-	Asp C:243

(no "SAP(SNP)/Variant" information available for 4KNW)

(no "PROSITE Motif" information available for 4KNW)

(no "Exon" information available for 4KNW)

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:239
                                                                                                                                                                                                                                                                               
               SCOP domains d4knwa_ A: automated matches                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.......hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhhhh.eeee.hhh.....hhhhhhhhhhhh..hhh.eeeee....hhhhhhhhh...eeeee...............eee.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4knw A   6 SRVRAVFFDLDNTLIDTAGASRRGMLEVIKLLQSKYHYKEEAEIICDKVQVKLSKECFHPYNTCITDLRTSHWEEAIQETKGGAANRKLAEECYFLWKSTRLQHMTLAEDVKAMLTELRKEVRLLLLTNGDRQTQREKIEACACQSYFDAVVVGGEQREEKPAPSIFYYCCNLLGVQPGDCVMVGDTLETDIQGGLNAGLKATVWINKNGIVPLKSSPVPHYMVSSVLELPALLQSIDC 244
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235

Chain B from PDB  Type:PROTEIN  Length:240
                                                                                                                                                                                                                                                                                
               SCOP domains d4knwb_ B: automated matches                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee.......hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhhhh.eeee.hhh.....hhhhhhhhhhhhh.hhh.eeeee....hhhhhhhhhh..eeeee...............eee.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4knw B   6 SRVRAVFFDLDNTLIDTAGASRRGMLEVIKLLQSKYHYKEEAEIICDKVQVKLSKECFHPYNTCITDLRTSHWEEAIQETKGGAANRKLAEECYFLWKSTRLQHMTLAEDVKAMLTELRKEVRLLLLTNGDRQTQREKIEACACQSYFDAVVVGGEQREEKPAPSIFYYCCNLLGVQPGDCVMVGDTLETDIQGGLNAGLKATVWINKNGIVPLKSSPVPHYMVSSVLELPALLQSIDCK 245
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245

Chain C from PDB  Type:PROTEIN  Length:238
                                                                                                                                                                                                                                                                              
               SCOP domains d4knwc_ C: automated matches                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.......hhhhhhhhhhhhhhhhhhh......hhhhhh.................hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhhh..hhh.eeeee....hhhhhhhhh...eeeee...............eee.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4knw C   6 SRVRAVFFDLDNTLIDTAGASRRGMLEVIKLLQSKYHYKEEAEIICDKVQVKLSKECFHPYNTCITDLRTSHWEEAIQETKGGAANRKLAEECYFLWKSTRLQHMTLAEDVKAMLTELRKEVRLLLLTNGDRQTQREKIEACACQSYFDAVVVGGEQREEKPAPSIFYYCCNLLGVQPGDCVMVGDTLETDIQGGLNAGLKATVWINKNGIVPLKSSPVPHYMVSSVLELPALLQSID 243
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235

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: beta-Phosphoglucomutase-like (27)

Protein domain: automated matches (4)

Human (Homo sapiens) [TaxId: 9606] (3)

1a	d4knwa_	A:
1b	d4knwb_	B:
1c	d4knwc_	C:

(no "CATH Domain" information available for 4KNW)

(no "Pfam Domain" information available for 4KNW)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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		VO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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		AC2	[ RasMol ]	+environment [ RasMol ]
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		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu B:61 - Cys B:62	[ RasMol ]
		His A:64 - Pro A:65	[ RasMol ]
		His B:64 - Pro B:65	[ RasMol ]
		Ile C:242 - Asp C:243	[ RasMol ]
		Lys A:166 - Pro A:167	[ RasMol ]
		Lys B:166 - Pro B:167	[ RasMol ]
		Lys C:166 - Pro C:167	[ RasMol ]
		Phe C:63 - His C:64	[ RasMol ]
		Ser C:6 - Arg C:7	[ RasMol ]
		Thr A:68 - Cys A:69	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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	4knw
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	3.1.3.29
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	NANP_HUMAN \| Q8TBE9	:	2w4m 4knv

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (1, 3)

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Gene Ontology (9, 9)

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