2IC8 - JenaLib

Title :   CRYSTAL STRUCTURE OF GLPG

Authors :   Y. Ha

Date :   12 Sep 06 (Deposition) - 17 Oct 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A

Keywords :   Rhomboid, Intramembrane Proteolysis, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Wang, Y. Zhang, Y. Ha
Crystal Structure Of A Rhomboid Family Intramembrane Protease.
Nature V. 444 179 2006
PubMed-ID: 17051161 | Reference-DOI: 10.1038/NATURE05255
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 12)

Sites (12, 12)

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HOH A:14 , HOH A:27 , GLU A:91 , ARG A:92 , ALA A:93 , TRP A:157 , TRP A:159 , TYR A:160 , GLY A:163 , ALA A:164 , BNG A:502	BINDING SITE FOR RESIDUE BNG A 501
02	AC2	SOFTWARE	HOH A:27 , GLN A:226 , BNG A:501	BINDING SITE FOR RESIDUE BNG A 502
03	AC3	SOFTWARE	PHE A:133 , THR A:178 , BNG A:504	BINDING SITE FOR RESIDUE BNG A 503
04	AC4	SOFTWARE	PHE A:135 , PHE A:139 , BNG A:503 , BNG A:505	BINDING SITE FOR RESIDUE BNG A 504
05	AC5	SOFTWARE	MET A:100 , TRP A:136 , PHE A:139 , ALA A:182 , BNG A:504	BINDING SITE FOR RESIDUE BNG A 505
06	AC6	SOFTWARE	LEU A:148 , MET A:149 , PHE A:153 , PHE A:232	BINDING SITE FOR RESIDUE BNG A 506
07	AC7	SOFTWARE	ALA A:250 , GLY A:252 , BNG A:510	BINDING SITE FOR RESIDUE BNG A 507
08	AC8	SOFTWARE	ILE A:109 , LEU A:234 , ILE A:237 , VAL A:238 , TRP A:241	BINDING SITE FOR RESIDUE BNG A 508
09	AC9	SOFTWARE	ARG A:92 , TRP A:98 , ILE A:102 , TRP A:212 , GLU A:216 , ARG A:227 , ILE A:230	BINDING SITE FOR RESIDUE BNG A 509
10	BC1	SOFTWARE	PHE A:192 , VAL A:267 , LEU A:270 , BNG A:507	BINDING SITE FOR RESIDUE BNG A 510
11	BC2	SOFTWARE	TRP A:122	BINDING SITE FOR RESIDUE BNG A 511
12	BC3	SOFTWARE	HOH A:11 , PHE A:127 , PRO A:129 , LYS A:132 , LEU A:169 , GLY A:170 , SER A:171 , GLY A:172	BINDING SITE FOR RESIDUE BNG A 512

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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

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:182
 aligned with GLPG_ECOLI | P09391 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:182
                                   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270  
           GLPG_ECOLI    91 ERAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMANGAHIAGLAVGLAMAFVDSLNA 272
               SCOP domains d2ic8a1 A:91-272 GlpG                                                                                                                                                                  SCOP domains
               CATH domains 2ic8A00 A:91-272 Rhomboid-like domains                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ic8 A  91 ERAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMANGAHIAGLAVGLAMAFVDSLNA 272
                                   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270

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 (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (GLPG_ECOLI | P09391)

molecular function
	GO:0004175	endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
	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: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.
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
	GO:0016485	protein processing	Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
	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:0005887	integral component of plasma membrane	The component of the plasma 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.

Visualization

Interactive Views

Asymmetric/Biological 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
		BNG	[ 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 ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ic8)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2ic8
		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
	GLPG_ECOLI \| P09391
		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)
	(no 'Enzyme Classificator' available)
		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

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	GLPG_ECOLI \| P09391
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description