4PRU - JenaLib

Title :   CRYSTAL STRUCTURE OF DIMETHYLLYSINE HEN EGG-WHITE LYSOZYME IN COMPLEX WITH SCLX4 AT 2.2 A RESOLUTION

Authors :   R. E. Mcgovern, J. A. Lyons, P. B. Crowley

Date :   06 Mar 14 (Deposition) - 12 Nov 14 (Release) - 21 Jan 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Hydrolase(O-Glycosyl), Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. E. Mcgovern, B. D. Snarr, J. A. Lyons, J. Mcfarlane, A. L. Whiting, I. Paci, F. Hof, P. B. Crowley
Structural Study Of A Small Molecule Receptor Bound To Dimethyllysine In Lysozyme.
Chem Sci V. 6 442 2015
PubMed-ID: 25530835 | Reference-DOI: 10.1039/C4SC02383H

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 18)

Asymmetric Unit (4, 18)

No.	Name	Count	Type	Full Name
1	DM0	2	Mod. Amino Acid	N~2~,N~2~,N~6~,N~6~-TETRAMETHYL-L-LYSINE
2	GOL	2	Ligand/Ion	GLYCEROL
3	MLY	10	Mod. Amino Acid	N-DIMETHYL-LYSINE
4	T3Y	4	Ligand/Ion	25,26,27,28-TETRAHYDROXYPENTACYCLO[19.3.1.1~3,7~.1~9,13~.1~15,19~]OCTACOSA-1(25),3(28),4,6,9(27),10,12,15(26),16,18,21,23-DODECAENE-5,11,17,23-TETRASULFONICACID

Biological Unit 1 (4, 10)

No.	Name	Count	Type	Full Name
1	DM0	1	Mod. Amino Acid	N~2~,N~2~,N~6~,N~6~-TETRAMETHYL-L-LYSINE
2	GOL	2	Ligand/Ion	GLYCEROL
3	MLY	5	Mod. Amino Acid	N-DIMETHYL-LYSINE
4	T3Y	2	Ligand/Ion	25,26,27,28-TETRAHYDROXYPENTACYCLO[19.3.1.1~3,7~.1~9,13~.1~15,19~]OCTACOSA-1(25),3(28),4,6,9(27),10,12,15(26),16,18,21,23-DODECAENE-5,11,17,23-TETRASULFONICACID

Biological Unit 2 (3, 8)

No.	Name	Count	Type	Full Name
1	DM0	1	Mod. Amino Acid	N~2~,N~2~,N~6~,N~6~-TETRAMETHYL-L-LYSINE
2	GOL	-1	Ligand/Ion	GLYCEROL
3	MLY	5	Mod. Amino Acid	N-DIMETHYL-LYSINE
4	T3Y	2	Ligand/Ion	25,26,27,28-TETRAHYDROXYPENTACYCLO[19.3.1.1~3,7~.1~9,13~.1~15,19~]OCTACOSA-1(25),3(28),4,6,9(27),10,12,15(26),16,18,21,23-DODECAENE-5,11,17,23-TETRASULFONICACID

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:23 , ASN A:106 , TRP A:111 , ARG A:112 , MLY A:116 , GLY A:117 , GOL A:203 , HOH A:310 , HOH A:327 , HOH A:347 , ARG B:5 , MLY B:33 , PHE B:38 , PRO B:70 , GLY B:71 , TRP B:123	BINDING SITE FOR RESIDUE T3Y A 201
2	AC2	SOFTWARE	DM0 A:1 , PHE A:3 , GLU A:7 , ALA A:10 , ALA A:11 , ARG A:14 , HIS A:15 , ARG A:128 , HOH A:306 , HOH A:340 , HOH A:346	BINDING SITE FOR RESIDUE T3Y A 202
3	AC3	SOFTWARE	ASN A:27 , CYS A:115 , GLY A:117 , THR A:118 , VAL A:120 , T3Y A:201 , ARG B:114	BINDING SITE FOR RESIDUE GOL A 203
4	AC4	SOFTWARE	PHE A:34 , ARG A:114 , THR A:118 , ASP A:119 , TRP A:123 , T3Y B:201	BINDING SITE FOR RESIDUE GOL A 204
5	AC5	SOFTWARE	ARG A:5 , MLY A:33 , GLY A:71 , SER A:72 , ARG A:73 , TRP A:123 , GOL A:204 , HOH A:312 , ASN B:106 , TRP B:111 , ARG B:112 , MLY B:116 , GLY B:117 , HOH B:303 , HOH B:304 , HOH B:321 , HOH B:327 , HOH B:333 , HOH B:337	BINDING SITE FOR RESIDUE T3Y B 201
6	AC6	SOFTWARE	DM0 B:1 , PHE B:3 , GLU B:7 , ALA B:10 , ALA B:11 , ARG B:14 , HIS B:15 , HOH B:311 , HOH B:316 , HOH B:346 , HOH B:347	BINDING SITE FOR RESIDUE T3Y B 202

SS Bonds (8, 8)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:129
                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....eee.....eee....ee...................hhhhhhh..hhhhhhhhhhhhhh......hhhhhhhh...hhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pru A   1 kVFGRCELAAAMkRHGLDNYRGYSLGNWVCAAkFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAkkIVSDGNGMNAWVAWRNRCkGTDVQAWIRGCRL 129
                            |       10  |     20        30  |     40        50        60        70        80        90     ||100       110     | 120         
                            |          13-MLY              33-MLY                                                         96-MLY             116-MLY         
                            1-DM0                                                                                          97-MLY

Chain B from PDB  Type:PROTEIN  Length:129
                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....eee.....eee....ee...................hhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pru B   1 kVFGRCELAAAMkRHGLDNYRGYSLGNWVCAAkFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAkkIVSDGNGMNAWVAWRNRCkGTDVQAWIRGCRL 129
                            |       10  |     20        30  |     40        50        60        70        80        90     ||100       110     | 120         
                            1-DM0      13-MLY              33-MLY                                                         96-MLY             116-MLY         
                                                                                                                           97-MLY

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (13, 13)

Visualization

Interactive Views

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		DM0	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MLY	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		T3Y	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asp A:101 - Gly A:102	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	4pru
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	LYSC_CHICK \| P00698
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.2.1.17
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description