4KNV - JenaLib

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Title :   THE CRYSTAL STRUCTURE OF APO HUMAN HDHD4 FROM SE-MAD

Authors :   H. E. Klei

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

Method :   X-RAY DIFFRACTION

Resolution :   1.99

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (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
	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
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 16)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
3	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 7)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (2, 7)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:12 , LEU A:13 , ASP A:14 , THR A:131 , ASN A:132 , LYS A:164 , MG A:302 , HOH A:401 , HOH A:412	BINDING SITE FOR RESIDUE PO4 A 301
2	AC2	SOFTWARE	ASP A:12 , ASP A:14 , ASP A:189 , PO4 A:301 , HOH A:402 , HOH A:412	BINDING SITE FOR RESIDUE MG A 302
3	AC3	SOFTWARE	ASP B:12 , LEU B:13 , ASP B:14 , THR B:131 , ASN B:132 , LYS B:164 , MG B:302 , HOH B:401 , HOH B:434 , HOH B:476	BINDING SITE FOR RESIDUE PO4 B 301
4	AC4	SOFTWARE	ASP B:12 , ASP B:14 , ASP B:189 , PO4 B:301 , HOH B:402 , HOH B:448	BINDING SITE FOR RESIDUE MG B 302

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

Asymmetric Unit

No.	Residues
1	Lys A:164	-	Pro A:165
2	Lys B:164	-	Pro B:165

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

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

(no "Exon" information available for 4KNV)

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:241
                                                                                                                                                                                                                                                                                 
               SCOP domains d4knva_ A: automated matches                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.......hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhh.hhhhh.eeee.hhh.....hhhhhhhhhhhh..hhh.eeeee....hhhhhhhhh...eeeee...............eee.hhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4knv A   6 mRAVFFDLDNTLIDTAGASRRGmLEVIKLLQSKYHYKEEAEIICDKVQVKLSKECFHPYNTCITDLRTSHWEEAIQETKGGAANRKLAEECYFLWKSTRLQHmTLAEDVKAmLTELRKEVRLLLLTNGDRQTQREKIEACACQSYFDAVVVGGEQREEKPAPSIFYYCCNLLGVQPGDCVmVGDTLETDIQGGLNAGLKATVWINKNGIVPLKSSPVPHYmVSSVLELPALLQSIDCLVPR 246
                            |       15        25  |     35        45        55        65        75        85        95       105  |    115 |     125       135       145       155       165       175       185|      195       205       215       225|      235       245 
                            |                    28-MSE                                                                         108-MSE  117-MSE                                                              186-MSE                                 226-MSE                
                            6-MSE

Chain B from PDB  Type:PROTEIN  Length:234
                                                                                                                                                                                                                                                                          
               SCOP domains d4knvb_ B: automated matches                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee.......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh...eeeeee..hhhhhhhhhhhh.hhhhh.eeee.hhh.....hhhhhhhhhhhhh.hhh.eeeee....hhhhhhhhh...eeeee...............eee.hhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4knv B   6 mRAVFFDLDNTLIDTAGASRRGmLEVIKLLQSKYHYKEEAEIICDKVQVKLSKECITDLRTSHWEEAIQETKGGAANRKLAEECYFLWKSTRLQHmTLAEDVKAmLTELRKEVRLLLLTNGDRQTQREKIEACACQSYFDAVVVGGEQREEKPAPSIFYYCCNLLGVQPGDCVmVGDTLETDIQGGLNAGLKATVWINKNGIVPLKSSPVPHYmVSSVLELPALLQSIDCLVPR 246
                            |       15        25  |     35        45        55   ||   72        82        92       102     | 112    |  122       132       142       152       162       172       182   |   192       202       212       222   |   232       242    
                            6-MSE                28-MSE                         59|                                      108-MSE  117-MSE                                                              186-MSE                                 226-MSE                
                                                                                 67

Legend:		→ Mismatch	(orange background)
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	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( (-)

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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	d4knva_	A:
1b	d4knvb_	B:

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

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

Asymmetric Unit(hide GO term definitions)

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	Cis Peptide Bonds
		Lys A:164 - Pro A:165	[ RasMol ]
		Lys B:164 - Pro B:165	[ RasMol ]

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	NANP_HUMAN \| Q8TBE9	:	2w4m 4knw

Description

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Ligands, Modified Residues, Ions (3, 16)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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