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(-) Description

Title :  GROUND STATE OF BACTERIORHODOPSIN FROM HALOBACTERIUM SALINARUM
 
Authors :  V. Borshchevskiy, I. Erofeev, E. Round, M. Weik, A. Ishchenko, I. Gushc A. Mishin, G. Bueldt, V. Gordeliy
Date :  22 Aug 13  (Deposition) - 08 Oct 14  (Release) - 10 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (3x)
Keywords :  Seven Transmembrane Helix/Bacterial Rhodopsins, Proton Pumping, Membrane, Transport Protein, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Borshchevskiy, E. Round, I. Erofeev, M. Weik, A. Ishchenko, I. Gushchin, A. Mishin, D. Willbold, G. Bueldt, V. Gordeliy
Low-Dose X-Ray Radiation Induces Structural Alterations In Proteins
Acta Crystallogr. , Sect. D V. 70 2675 2014
PubMed-ID: 22174747  |  Reference-DOI: 10.1107/S1399004714017295

(-) Compounds

Molecule 1 - BACTERIORHODOPSIN
    Chains: A
    Organism Scientific: HALOBACTERIUM SP. NRC-1
    Organism Taxid: 64091
    Strain: S9
    Synonym: BR, BACTERIOOPSIN, BO

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 20)

Asymmetric Unit (3, 20)
No.NameCountTypeFull Name
1L2P18Ligand/Ion2,3-DI-PHYTANYL-GLYCEROL
2RET1Ligand/IonRETINAL
3SQL1Ligand/Ion(6E,10E,14E,18E)-2,6,10,15,19,23-HEXAMETHYLTETRACOSA-2,6,10,14,18,22-HEXAENE
Biological Unit 1 (3, 20)
No.NameCountTypeFull Name
1L2P18Ligand/Ion2,3-DI-PHYTANYL-GLYCEROL
2RET1Ligand/IonRETINAL
3SQL1Ligand/Ion(6E,10E,14E,18E)-2,6,10,15,19,23-HEXAMETHYLTETRACOSA-2,6,10,14,18,22-HEXAENE
Biological Unit 2 (3, 60)
No.NameCountTypeFull Name
1L2P54Ligand/Ion2,3-DI-PHYTANYL-GLYCEROL
2RET3Ligand/IonRETINAL
3SQL3Ligand/Ion(6E,10E,14E,18E)-2,6,10,15,19,23-HEXAMETHYLTETRACOSA-2,6,10,14,18,22-HEXAENE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:132 , ALA A:139BINDING SITE FOR RESIDUE L2P A 1001
02AC2SOFTWARETYR A:26 , VAL A:213 , GLY A:218 , ARG A:225BINDING SITE FOR RESIDUE SQL A 1002
03AC3SOFTWAREILE A:52 , GLY A:116BINDING SITE FOR RESIDUE L2P A 1003
04AC4SOFTWARETRP A:80BINDING SITE FOR RESIDUE L2P A 1004
05AC5SOFTWARETYR A:64 , LEU A:123BINDING SITE FOR RESIDUE L2P A 1005
06AC6SOFTWARETYR A:131BINDING SITE FOR RESIDUE L2P A 1006
07AC7SOFTWAREVAL A:188 , ILE A:191BINDING SITE FOR RESIDUE L2P A 1009
08AC8SOFTWARELEU A:87 , PRO A:91BINDING SITE FOR RESIDUE L2P A 1010
09AC9SOFTWAREMET A:145 , VAL A:179 , SER A:183BINDING SITE FOR RESIDUE L2P A 1011
10BC1SOFTWARETYR A:147 , TYR A:150 , L2P A:1019BINDING SITE FOR RESIDUE L2P A 1012
11BC2SOFTWAREVAL A:173BINDING SITE FOR RESIDUE L2P A 1014
12BC3SOFTWARETRP A:10 , ILE A:11 , LEU A:15BINDING SITE FOR RESIDUE L2P A 1017
13BC4SOFTWAREILE A:198BINDING SITE FOR RESIDUE L2P A 1018
14BC5SOFTWARETHR A:24 , LEU A:25 , LEU A:28 , LYS A:40 , ALA A:44 , THR A:47 , LEU A:48 , ALA A:51 , PHE A:54 , ALA A:110 , ALA A:114 , TYR A:147 , L2P A:1012 , HOH A:1129BINDING SITE FOR RESIDUE L2P A 1019
15BC6SOFTWARETRP A:86 , THR A:90 , MET A:118 , SER A:141 , THR A:142 , TRP A:182 , TYR A:185 , TRP A:189 , ASP A:212 , LYS A:216BINDING SITE FOR RESIDUE RET A 1020

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4MD2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4MD2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MD2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MD2)

(-) Exons   (0, 0)

(no "Exon" information available for 4MD2)

(-) 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:224
                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4md2 A   5 TGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGEAE 234
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154 ||    170       180       190       200       210       220       230    
                                                                                                                                                                                 156|                                                                       
                                                                                                                                                                                  163
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4MD2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MD2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MD2)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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  4md2
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  BACR_HALSA | P02945
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        BACR_HALSA | P02945: 1ap9 1at9 1bac 1bad 1bct 1bha 1bhb 1bm1 1brd 1brr 1brx 1c3w 1c8r 1c8s 1cwq 1dze 1e0p 1f4z 1f50 1fbb 1fbk 1iw6 1iw9 1ixf 1jv6 1jv7 1kg8 1kg9 1kgb 1kme 1l0m 1m0k 1m0l 1m0m 1mgy 1o0a 1p8h 1p8i 1p8u 1pxr 1pxs 1py6 1q5i 1q5j 1qhj 1qko 1qkp 1qm8 1r2n 1r84 1s51 1s52 1s53 1s54 1s8j 1s8l 1tn0 1tn5 1ucq 1vjm 1x0i 1x0k 1x0s 1xji 2at9 2brd 2i1x 2i20 2i21 2ntu 2ntw 2wjk 2wjl 2zfe 2zzl 3coc 3cod 3han 3hao 3hap 3haq 3har 3has 3mbv 3ns0 3nsb 3t45 3utv 3utw 3utx 3uty 3vhz 3vi0 4fpd 4hwl 4hyx 4md1 4ov0 4x31 4x32 4xxj 5a44 5a45 5b34 5b35 5b6v 5b6w 5b6x 5b6y 5b6z 5br2 5br5 5h2h 5h2i 5h2j 5h2k 5h2l 5h2m 5h2n 5h2o 5h2p 5j7a 5vn7 5vn9

(-) Related Entries Specified in the PDB File

4md1 ORANGE SPECIES OF BACTERIORHODOPSIN FROM HALOBACTERIUM SALINARUM