4HBF - JenaLib

Title :   CRYSTAL STRUCTURE OF PPCA V13A MUTANT

Authors :   P. R. Pokkuluri, M. Schiffer

Date :   27 Sep 12 (Deposition) - 31 Oct 12 (Release) - 31 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. R. Pokkuluri, M. Schiffer
V13 Mutants Of Ppca
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	DXC	1	Ligand/Ion	(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID
2	HEM	3	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 7)

No.	Name	Count	Type	Full Name
1	DXC	1	Ligand/Ion	(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID
2	HEM	3	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 14)

No.	Name	Count	Type	Full Name
1	DXC	2	Ligand/Ion	(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID
2	HEM	6	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	SO4	6	Ligand/Ion	SULFATE ION

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:1 , ASP A:2 , ASP A:3 , ILE A:4 , PHE A:15 , HIS A:17 , GLN A:21 , VAL A:24 , CYS A:27 , CYS A:30 , HIS A:31 , ILE A:38 , GLU A:39 , CYS A:65 , LYS A:71 , HEM A:73 , DXC A:75 , HOH A:129 , HOH A:139 , HOH A:173	BINDING SITE FOR RESIDUE HEM A 72
2	AC2	SOFTWARE	LYS A:14 , HIS A:20 , ALA A:23 , VAL A:24 , GLY A:50 , CYS A:51 , CYS A:54 , HIS A:55 , LYS A:60 , PRO A:62 , HEM A:72 , HOH A:120 , HOH A:132 , HOH A:134	BINDING SITE FOR RESIDUE HEM A 73
3	AC3	SOFTWARE	ALA A:1 , ASP A:2 , LEU A:6 , ALA A:8 , LYS A:9 , ASN A:10 , GLU A:32 , GLY A:36 , PHE A:41 , GLY A:42 , LYS A:43 , ALA A:46 , HIS A:47 , LYS A:52 , HIS A:55 , PRO A:62 , THR A:63 , LYS A:64 , CYS A:65 , CYS A:68 , HIS A:69 , HOH A:101 , HOH A:122 , HOH A:147	BINDING SITE FOR RESIDUE HEM A 74
4	AC4	SOFTWARE	ILE A:4 , LEU A:6 , LYS A:29 , LYS A:37 , ILE A:38 , PHE A:41 , MET A:45 , GLY A:50 , HEM A:72 , HOH A:101 , HOH A:106 , HOH A:108 , HOH A:110	BINDING SITE FOR RESIDUE DXC A 75
5	AC5	SOFTWARE	HIS A:31 , GLU A:32 , GLY A:36 , LYS A:37 , ILE A:38 , GLU A:39 , HOH A:109	BINDING SITE FOR RESIDUE SO4 A 76
6	AC6	SOFTWARE	LYS A:28 , GLU A:32 , LYS A:43 , HIS A:47 , HOH A:149 , HOH A:167	BINDING SITE FOR RESIDUE SO4 A 77
7	AC7	SOFTWARE	GLY A:42 , LYS A:43 , GLU A:44 , HOH A:119 , HOH A:173	BINDING SITE FOR RESIDUE SO4 A 78

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 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:71
                                                                                                      
               SCOP domains d4hbfa_ A: automated matches                                            SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee......eeehhhhhhhhh.hhhhh.....hhhhhhhhhhhhh..hhhhhhhh.....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  4hbf A  1 ADDIVLKAKNGDAKFPHKAHQKAVPDCKKCHEKGPGKIEGFGKEMAHGKGCKGCHEEMKKGPTKCGECHKK 71
                                    10        20        30        40        50        60        70

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 (0, 0)

Pfam Domains (0, 0)

Gene Ontology (4, 4)

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
		DXC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		HEM	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ 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 ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4hbf)

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

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	4hbf
		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
	Q8GGK7_GEOSN \| Q8GGK7
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

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
	Q8GGK7_GEOSN \| Q8GGK7
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description