4P8W - JenaLib

Title :   THE CRYSTAL STRUCTURES OF YKL-39 IN THE PRESENCE OF CHITOOLIGOSACCHARIDES (GLCNAC4) WERE SOLVED TO RESOLUTIONS OF 1.9 ANGSTROM

Authors :   W. Suginta, A. Ranok, R. C. Robinson, J. Wongsantichon

Date :   01 Apr 14 (Deposition) - 03 Dec 14 (Release) - 11 Feb 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.87

Chains :   Asym./Biol. Unit : A

Keywords :   Chitinase 3-Like Protein 2, Human Ykl-39, Family-18 Chitinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Ranok, J. Wongsantichon, R. C. Robinson, W. Suginta
Structural And Thermodynamic Insights Into Chitooligosaccharide Binding To Human Cartilage Chitinase 3-Like Protein 2 (Chi3L2 Or Ykl-39).
J. Biol. Chem. V. 290 2617 2015
PubMed-ID: 25477513 | Reference-DOI: 10.1074/JBC.M114.588905

Compounds

Molecule 1 - CHITINASE-3-LIKE PROTEIN 2
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET32A(+)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	CHI3L2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CHONDROCYTE PROTEIN 39,YKL-39

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Asymmetric/Biological Unit (3, 9)

No.	Name	Count	Type	Full Name
1	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
3	SO4	5	Ligand/Ion	SULFATE ION

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:232 , GLY A:238 , SER A:241 , LYS A:312 , ASN A:373 , HOH A:555 , HOH A:564	binding site for residue SO4 A 401
2	AC2	SOFTWARE	SER A:117 , SER A:118 , ARG A:121	binding site for residue SO4 A 402
3	AC3	SOFTWARE	LYS A:175 , ARG A:385 , HOH A:509 , HOH A:717	binding site for residue SO4 A 403
4	AC4	SOFTWARE	GLY A:107 , SER A:108 , LYS A:109 , HOH A:688	binding site for residue SO4 A 404
5	AC5	SOFTWARE	SER A:65 , LYS A:74 , PHE A:106 , HOH A:655 , HOH A:725 , HOH A:726 , HOH A:791	binding site for residue SO4 A 405
6	AC6	SOFTWARE	TYR A:32 , TRP A:36 , GLY A:103 , TYR A:104 , LEU A:105 , SER A:143 , ILE A:145 , TYR A:146 , LEU A:210 , PHE A:212 , ASP A:213 , TRP A:218 , TYR A:269 , PHE A:301 , TRP A:360 , MET A:364 , HOH A:614 , HOH A:615 , HOH A:619 , HOH A:626 , HOH A:635 , HOH A:637 , HOH A:641 , HOH A:668 , HOH A:711 , HOH A:740 , HOH A:769 , HOH A:790 , HOH A:825	binding site for Poly-Saccharide residues NDG A 406 through NAG A 409

SS Bonds (2, 2)

Cis Peptide Bonds (6, 6)

Asymmetric/Biological Unit

No.	Residues
1	Glu A:42	-	Pro A:43
2	Ser A:62	-	Phe A:63
3	His A:112	-	Pro A:113
4	Ile A:145	-	Tyr A:146
5	Lys A:220	-	Pro A:221
6	Trp A:360	-	Ser A:361

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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

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Chain A from PDB  Type:PROTEIN  Length:364
                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhh......hhhhh......eeeeeeeeee..eee....hhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhhhhhh.eeeee..........................hhhhhhhhhhhhhhhhhhh..hhh.eeeeee.eeeeeee..........eeee...........eeehhhhhhhh...eeeee....eeeeee..eeee..hhhhhhhhhhhhhhh...eeeeehhhhh...........hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p8w A  27 YKLVCYFTNWSQDRQEPGKFTPENIDPFLCSHLIYSFASIENNKVIIKDKSEVMLYQTINSLKTKNPKLKILLSIGGYLFGSKGFHPMVDSSTSRLEFINSIILFLRNHNFDGLDVSWIYPDQKENTHFTVLIHELAEAFQKDFTKSTKERLLLTVGVSAGRQMIDNSYQVEKLAKDLDFINLLSFDFHGSWEKPLITGHNSPLSKGWQDRGPSSYYNVEYAVGYWIHKGMPSEKVVMGIPTYGHSFTLASAETTVGAPASGPGAAGPITESSGFLAYYEICQFLKGAKITWLQDQQVPYAVKGNQWVGYDDVKSMETKVQFLKNLNLGGAMIWSIDMDDFTGKSCNQGPYPLVQAVKRSLGSL 390
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386

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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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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	Cis Peptide Bonds
		Glu A:42 - Pro A:43	[ RasMol ]
		His A:112 - Pro A:113	[ RasMol ]
		Ile A:145 - Tyr A:146	[ RasMol ]
		Lys A:220 - Pro A:221	[ RasMol ]
		Ser A:62 - Phe A:63	[ RasMol ]
		Trp A:360 - Ser A:361	[ RasMol ]

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	4p8w
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