3WKM - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   THE PERIPLASMIC PDZ TANDEM FRAGMENT OF THE RSEP HOMOLOGUE FROM AQUIFEX AEOLICUS IN COMPLEX WITH THE FAB FRAGMENT

Authors :   T. Nogi, S. Tabata, K. Tamura-Kawakami, J. Takagi

Date :   28 Oct 13 (Deposition) - 18 Dec 13 (Release) - 19 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B,H,I,L,M
Biol. Unit 1: A,H,L  (1x)
Biol. Unit 2: B,I,M  (1x)

Keywords :   Pdz Domain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Hizukuri, T. Oda, S. Tabata, K. Tamura-Kawakami, R. Oi, M. Sato, J. Takagi, Y. Akiyama, T. Nogi
A Structure-Based Model Of Substrate Discrimination By A Noncanonical Pdz Tandem In The Intramembrane-Cleaving Protease Rsep
Structure V. 22 326 2013
PubMed-ID: 24389025 | Reference-DOI: 10.1016/J.STR.2013.12.003

Molecule 1 - PUTATIVE ZINC METALLOPROTEASE AQ_1964
	Chains	:	A, B
	EC Number	:	3.4.24.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	PDZ TANDEM FRAGMENT, UNP RESIDUES 115-292
	Gene	:	AQ_1964
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	224324
	Strain	:	VF5

Molecule 2 - MOUSE IGG1-KAPPA FAB (HEAVY CHAIN)
	Chains	:	H, I
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 3 - MOUSE IGG1-KAPPA FAB (LIGHT CHAIN)
	Chains	:	L, M
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	H	I	L	M
Biological Unit 1 (1x)	:	A		H		L
Biological Unit 2 (1x)	:		B		I		M

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3WKM)

(no "Site" information available for 3WKM)

Asymmetric Unit

No.	Residues
1	H:22	-	H:96
2	H:150	-	H:205
3	I:22	-	I:96
4	I:150	-	I:205
5	L:23	-	L:92
6	L:138	-	L:198
7	M:23	-	M:92
8	M:138	-	M:198

Asymmetric Unit

No.	Residues
1	Phe H:156	-	Pro H:157
2	Glu H:158	-	Pro H:159
3	Trp H:198	-	Pro H:199
4	Ser L:7	-	Pro L:8
5	Asp L:80	-	Pro L:81
6	Asp L:98	-	Pro L:99
7	Tyr L:144	-	Pro L:145
8	Phe I:156	-	Pro I:157
9	Glu I:158	-	Pro I:159
10	Ser M:7	-	Pro M:8
11	Asp M:80	-	Pro M:81
12	Asp M:98	-	Pro M:99
13	Tyr M:144	-	Pro M:145

(no "SAP(SNP)/Variant" information available for 3WKM)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	Y1964_AQUAE	189-265	2	A:189-265 B:189-265

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	Y1964_AQUAE	189-265	1	A:189-265 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	Y1964_AQUAE	189-265	1	- B:189-265

(no "Exon" information available for 3WKM)

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:176
 aligned with Y1964_AQUAE | O67776 from UniProtKB/Swiss-Prot  Length:429

    Alignment length:176
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285      
          Y1964_AQUAE   116 VPKYLKEPVVVGYVQRDSIAQKIGIKPGDKIIKINGYEVRTWEDLRDALIRLSLDGVKETTLFLERNGEVLHLTIKVPNVQKGEELGIAPLVKPVVGGVKKGSPADQVGIKPGDLILEVNGKKINTWYELVEEVRKSQGKAIKLKILRNGKMIEKELIPAKDPKTGTYFIGLFPKT 291
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.ee..ee...hhhhhh......eeeee..ee..hhhhhhhhhhhhhhh...eeeeeeee..eeeeeeee..hhhhh....ee......eeee...hhhhhh......eeeee..ee..hhhhhhhhhhh.....eeeeeee..eeeeeee..eee....eee..eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------PDZ  PDB: A:189-265 UniProt: 189-265                                         -------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wkm A 116 VPKYLKEPVVVGYVQRDSIAQKIGIKPGDKIIKINGYEVRTWEDLRDALIRLSLDGVKETTLFLERNGEVLHLTIKVPNVQKGEELGIAPLVKPVVGGVKKGSPADQVGIKPGDLILEVNGKKINTWYELVEEVRKSQGKAIKLKILRNGKMIEKELIPAKDPKTGTYFIGLFPKT 291
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285

Chain B from PDB  Type:PROTEIN  Length:179
 aligned with Y1964_AQUAE | O67776 from UniProtKB/Swiss-Prot  Length:429

    Alignment length:179
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282         
          Y1964_AQUAE   113 GVEVPKYLKEPVVVGYVQRDSIAQKIGIKPGDKIIKINGYEVRTWEDLRDALIRLSLDGVKETTLFLERNGEVLHLTIKVPNVQKGEELGIAPLVKPVVGGVKKGSPADQVGIKPGDLILEVNGKKINTWYELVEEVRKSQGKAIKLKILRNGKMIEKELIPAKDPKTGTYFIGLFPKT 291
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh.ee..ee...hhhhhh......eeeee..ee..hhhhhhhhhhhhhhh...eeeeeeee..eeeeeeee..hhhhh....ee......eeee...hhhhhh......eeeee..ee..hhhhhhhhhhh.....eeeeeee..eeeeeee..ee......ee..eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------PDZ  PDB: B:189-265 UniProt: 189-265                                         -------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wkm B 113 GSEVPKYLKEPVVVGYVQRDSIAQKIGIKPGDKIIKINGYEVRTWEDLRDALIRLSLDGVKETTLFLERNGEVLHLTIKVPNVQKGEELGIAPLVKPVVGGVKKGSPADQVGIKPGDLILEVNGKKINTWYELVEEVRKSQGKAIKLKILRNGKMIEKELIPAKDPKTGTYFIGLFPKT 291
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282

Chain H from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeeeee.....eeeeee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3wkm H   1 EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYLHWVKQRPEHGLEWIGRIDPANGNAKYDPKFQDKATITADTSSNTAYLQLNSLTSEDTAVYYCSNRQLGLRGYYYAMDYWGQGTSVSVSSAKTTPPSVYPLAPGSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP 222
                                    10        20        30        40        50        60        70        80        90       100       110       120       130      |146       156       166       176       186       196       206       216      
                                                                                                                                                                  137|                                                                              
                                                                                                                                                                   144

Chain I from PDB  Type:PROTEIN  Length:194
                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeeee.......eeeee...eeeee........eeeee..eeeeeee.......ee.........ee...eee..eeeeeee..eeeee....eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wkm I   1 EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYLHWVKQRPEHGLEWIGRIDPANGNAKYDPKFQDKATITADTSSNTAYLQLNSLTSEDTAVYYCSNRQLGLRGYYYAMDYWGQGTSVSVSSAKTTPPSVYPLALGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTCNVAHPASSTKVDK 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    || 152       162       172       182       204       214    
                                                                                                                                                                135|                                        191|              
                                                                                                                                                                 148                                         204

Chain L from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains d3wkml1 L:1-111 automated matches                                                                              d3wkml2 L:112-215 automated matches                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee...........eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wkm L   1 YIVLTQSPVSLAVSLGQRATISCRASESVDSYGDSFMHWYQQKPGQPPKLLIYLASNLESGVPARFSGSGSRTDFTLTIDPVEADDAATYYCQQNNEDPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain M from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains d3wkmm1 M:1-111 automated matches                                                                              d3wkmm2 M:112-214 automated matches                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....ee..ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh..eeeeeeeeee.....eeeee....ee...eeeee.........eeeeeeeeehhhhhh....eeeeee.......eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wkm M   1 YIVLTQSPVSLAVSLGQRATISCRASESVDSYGDSFMHWYQQKPGQPPKLLIYLASNLESGVPARFSGSGSRTDFTLTIDPVEADDAATYYCQQNNEDPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFN 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: automated matches (864)

Protein domain: automated matches (864)

Mouse (Mus musculus) [TaxId: 10090] (360)

1a	d3wkml1	L:1-111
1b	d3wkml2	L:112-215
1c	d3wkmm1	M:1-111
1d	d3wkmm2	M:112-214

(no "CATH Domain" information available for 3WKM)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (Y1964_AQUAE | O67776)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004222	metalloendopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008237	metallopeptidase activity	Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric Unit
	Complete Structure
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3wkm)

	Sites
(no "Sites" information available for 3wkm)

	Cis Peptide Bonds
		Asp L:80 - Pro L:81	[ RasMol ]
		Asp L:98 - Pro L:99	[ RasMol ]
		Asp M:80 - Pro M:81	[ RasMol ]
		Asp M:98 - Pro M:99	[ RasMol ]
		Glu H:158 - Pro H:159	[ RasMol ]
		Glu I:158 - Pro I:159	[ RasMol ]
		Phe H:156 - Pro H:157	[ RasMol ]
		Phe I:156 - Pro I:157	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Ser M:7 - Pro M:8	[ RasMol ]
		Trp H:198 - Pro H:199	[ RasMol ]
		Tyr L:144 - Pro L:145	[ RasMol ]
		Tyr M:144 - Pro M:145	[ RasMol ]

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

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Access by PDB/NDB ID
	3wkm
		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
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Access by UniProt ID/Accession number
	Y1964_AQUAE \| O67776
		Comparative Protein Structure Models	:	ModBase
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		Protein-protein Interaction	:	DIP
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	3.4.24.-
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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		Disease Information	:	OMIM

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		Age Related Information	:	GenAge

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
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	Y1964_AQUAE \| O67776
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UniProtKB/Swiss-Prot
	Y1964_AQUAE \| O67776	:	3wkl

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (8, 8)

Cis Peptide Bonds (13, 13)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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