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(-) Description

Title :  CRYSTAL STRUCTURE OF PHARAONIS HALORHODOPSIN IN COMPLEX WITH AZIDE ION
 
Authors :  T. Kouyama, S. Kanada
Date :  24 Dec 09  (Deposition) - 02 Feb 11  (Release) - 02 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,D
Keywords :  Light-Driven Chloride Ion Pump, Trimeric Bacterioruberin-Protein Complex, Retinal Protein, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Kanada, T. Kouyama
Binding Mode Of Azide Ion To Pharaonis Halorhodopsin
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HALORHODOPSIN
    Chains: A, B, D
    Organism Scientific: NATRONOMONAS PHARAONIS
    Organism Taxid: 348780
    Other Details: STRAIN MK-1 WAS A HALORHODOPSIN-OVERPRODUCING MUTANT GENERATED FROM TYPE STRAIN D2160T.
    Strain: MK-1

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 17)

Asymmetric/Biological Unit (4, 17)
No.NameCountTypeFull Name
122B2Ligand/IonBACTERIORUBERIN
2AZI3Ligand/IonAZIDE ION
3L3P9Ligand/Ion2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE
4RET3Ligand/IonRETINAL

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:127 , THR A:131 , MET A:159 , TYR A:180 , SER A:183 , PHE A:187 , TRP A:222 , TYR A:225 , PRO A:226 , ASP A:252 , LYS A:256BINDING SITE FOR RESIDUE RET A 292
02AC2SOFTWAREILE A:49 , THR A:56 , LYS A:65 , ILE A:72 , PHE D:155 , ALA D:185 , VAL D:189 , ILE D:193BINDING SITE FOR RESIDUE 22B A 300
03AC3SOFTWAREVAL A:93 , TRP A:121 , LEU A:164 , LEU A:168 , L3P B:311BINDING SITE FOR RESIDUE L3P A 313
04AC4SOFTWAREALA A:80 , LEU A:89 , THR A:126 , VAL D:161 , THR D:162 , TRP D:179BINDING SITE FOR RESIDUE L3P A 317
05AC5SOFTWARETRP B:127 , THR B:131 , MET B:159 , TYR B:180 , SER B:183 , PHE B:187 , TRP B:222 , TYR B:225 , PRO B:226 , ASP B:252 , LYS B:256BINDING SITE FOR RESIDUE RET B 292
06AC6SOFTWAREVAL A:161 , LEU A:168 , L3P A:313 , GLN B:21 , ALA B:80 , LEU B:89 , TRP B:121 , THR B:126BINDING SITE FOR RESIDUE L3P B 311
07AC7SOFTWARESER B:92 , VAL B:93 , TRP B:121 , LEU B:164BINDING SITE FOR RESIDUE L3P B 315
08AC8SOFTWAREPHE B:150 , VAL D:77BINDING SITE FOR RESIDUE L3P B 318
09AC9SOFTWARESER A:78 , SER A:81 , THR A:126 , SER A:130 , LYS A:256 , HOH A:504BINDING SITE FOR RESIDUE AZI A 401
10BC1SOFTWARETRP D:127 , THR D:131 , MET D:159 , TYR D:180 , SER D:183 , PHE D:187 , TRP D:222 , TYR D:225 , PRO D:226 , LYS D:256BINDING SITE FOR RESIDUE RET D 292
11BC2SOFTWAREILE D:153 , THR D:154BINDING SITE FOR RESIDUE L3P D 312
12BC3SOFTWAREVAL B:161 , LEU B:164 , LEU B:168 , VAL D:19 , GLN D:21 , ALA D:80 , LEU D:89 , TRP D:121 , THR D:126 , HOH D:521BINDING SITE FOR RESIDUE L3P D 314
13BC4SOFTWARETHR A:147 , PHE A:155 , VAL A:189 , ILE B:49 , VAL B:53 , THR B:56 , ILE B:72BINDING SITE FOR RESIDUE 22B B 300
14BC5SOFTWARELEU D:125BINDING SITE FOR RESIDUE L3P D 316
15BC6SOFTWARESER B:78 , SER B:81 , THR B:126 , SER B:130 , LYS B:256BINDING SITE FOR RESIDUE AZI B 401
16BC7SOFTWARESER D:78 , SER D:81 , THR D:126 , TRP D:127 , SER D:130 , LYS D:256BINDING SITE FOR RESIDUE AZI D 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ABW)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ABW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ABW)

(-) Exons   (0, 0)

(no "Exon" information available for 3ABW)

(-) 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:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains d3abwa_ A: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh....eee......................eee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3abw A  18 EVTQRELFEFVLNDPLLASSLYINIALAGLSILLFVFMTRGLDDPRAKLIAVSTILVPVVSIASYTGLASGLTISVLEMPAGHFAEGSSVMLGGEEVDGVVTMWGRYLTWALSTPMILLALGLLAGSNATKLFTAITFDIAMCVTGLAAALTTSSHLMRWFWYAISCACFIVVLYILLVEWAQDAKAAGTADIFSTLKLLTVVMWLGYPIVWALGVEGVAVLPVGYTSWAYSALDIVAKYIFAFLLLNYLTSNEGVVSGS 277
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277


Chain B from PDB  Type:PROTEIN  Length:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains d3abwb_ B: automated matches                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh....eee......................eeehhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3abw B  18 EVTQRELFEFVLNDPLLASSLYINIALAGLSILLFVFMTRGLDDPRAKLIAVSTILVPVVSIASYTGLASGLTISVLEMPAGHFAEGSSVMLGGEEVDGVVTMWGRYLTWALSTPMILLALGLLAGSNATKLFTAITFDIAMCVTGLAAALTTSSHLMRWFWYAISCACFIVVLYILLVEWAQDAKAAGTADIFSTLKLLTVVMWLGYPIVWALGVEGVAVLPVGYTSWAYSALDIVAKYIFAFLLLNYLTSNEGVVSG 276
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267         


Chain D from PDB  Type:PROTEIN  Length:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains d3abwd_ D: automated matches                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh....eee......................eeehhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3abw D  18 EVTQRELFEFVLNDPLLASSLYINIALAGLSILLFVFMTRGLDDPRAKLIAVSTILVPVVSIASYTGLASGLTISVLEMPAGHFAEGSSVMLGGEEVDGVVTMWGRYLTWALSTPMILLALGLLAGSNATKLFTAITFDIAMCVTGLAAALTTSSHLMRWFWYAISCACFIVVLYILLVEWAQDAKAAGTADIFSTLKLLTVVMWLGYPIVWALGVEGVAVLPVGYTSWAYSALDIVAKYIFAFLLLNYLTSNEGVVSG 276
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267
   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, 3)

Asymmetric/Biological Unit
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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3a7k STRUCTURE OF PHARAONIS HALORHODOPSIN WITH CHLORIDE ION