Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE INITIATION MODULE OF LGRA IN THE THIOLATION STATE
 
Authors :  J. M. Reimer, M. N. Aloise, T. M. Schmeing
Date :  16 Nov 15  (Deposition) - 20 Jan 16  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Nrps, Formylation Domain, Adenylation Domain, Peptidyl Carrier Protein, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Reimer, M. N. Aloise, P. M. Harrison, T. M. Schmeing
Synthetic Cycle Of The Initiation Module Of A Formylating Nonribosomal Peptide Synthetase.
Nature V. 529 239 2016
PubMed-ID: 26762462  |  Reference-DOI: 10.1038/NATURE16503

(-) Compounds

Molecule 1 - LINEAR GRAMICIDIN SYNTHETASE SUBUNIT A
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 2-766
    Gene: LGRA
    Organism Scientific: BREVIBACILLUS PARABREVIS
    Organism Taxid: 54914

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
15S42Ligand/Ion[(3~{R})-4-[[3-[2-[[(2~{S})-2-AZANYL-3-METHYL-BUTANOYL]AMINO]ETHYLAMINO]-3-OXIDANYLIDENE-PROPYL]AMINO]-2,2-DIMETHYL-3-OXIDANYL-4-OXIDANYLIDENE-BUTYL] DIHYDROGEN PHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
15S41Ligand/Ion[(3~{R})-4-[[3-[2-[[(2~{S})-2-AZANYL-3-METHYL-BUTANOYL]AMINO]ETHYLAMINO]-3-OXIDANYLIDENE-PROPYL]AMINO]-2,2-DIMETHYL-3-OXIDANYL-4-OXIDANYLIDENE-BUTYL] DIHYDROGEN PHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
15S41Ligand/Ion[(3~{R})-4-[[3-[2-[[(2~{S})-2-AZANYL-3-METHYL-BUTANOYL]AMINO]ETHYLAMINO]-3-OXIDANYLIDENE-PROPYL]AMINO]-2,2-DIMETHYL-3-OXIDANYL-4-OXIDANYLIDENE-BUTYL] DIHYDROGEN PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:395 , ASP A:396 , TYR A:421 , TYR A:439 , GLY A:462 , GLY A:463 , ILE A:488 , LYS A:589 , ARG A:591 , GLY A:592 , TYR A:593 , ILE A:730 , MET A:733 , HOH A:908binding site for residue 5S4 A 801
2AC2SOFTWAREPHE B:395 , ASP B:396 , LYS B:420 , TYR B:439 , GLY B:462 , GLY B:463 , GLY B:482 , ILE B:488 , MET B:489 , ARG B:591 , GLY B:592 , TYR B:593 , ILE B:730binding site for residue 5S4 B 801

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5ES8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5ES8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5ES8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5ES8)

(-) Exons   (0, 0)

(no "Exon" information available for 5ES8)

(-) 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:759
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......hhhhhhhhhh..eeeee.......hhhhh...eeeee......hhhhhhhh...eeeee.......ee.hhhhhhhhh....eeeeee.........eeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhh.............eehhhhhhhhhhhh..hhhhhhhhhhhhh...........hhhhhhhhhhhhh...eeeee..eeeehhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhh...eeee...hhhhhh...eeee..hhhhh...............eeeeeee.......eeeeeehhhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhh..eee.hhhhhhhhh........eeeee.............eeeeee.hhhhh...eeee...........ee...eeeeee............eeeeeee.....ee..hhhhhhhheee......eeeeeeeeeee.....eeeeee....eee..eeehhhhhhhhhhh.....eeeeeeee.....eeeeeeee.....hhhhhhhhhhh..hhhhh..eeeee...........hhhhh.......hhhhhhhhhhhhhhh..........hhhhh.hhhhhhhhhhhhhhh....hhhhhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5es8 A   1 MGRILFLTTFMSKGNKVVRYLESLHHEVVICQEKVHAQSANLQEIDWIVSYAYGYILDKEIVSRFRGRIINLHPSLLPWNKGRDPVFWSVWDETPKGVTIHLIDEHVDTGDILVQEEIAFADEDTLLDCYNKANQAIEELFIREWENIVHGRIAPYRQTAGGTLHFKADRDFYKNLNMTTVRELLALKRLCAEPKRGEKPIDKTFHQLFEQQVEMTPDHVAVVDRGQSLTYKQLNERANQLAHHLRGKGVKPDDQVAIMLDKSLDMIVSILAVMKAGGAYVPIDPDYPGERIAYMLADSSAAILLTNALHEEKANGACDIIDVHDPDSYSENTNNLPHVNRPDDLVYVMYTSGSTGLAKGVMIEHHNLVNFCEWYRPYFGVTPADKALVYSSFSFDGSALDIFTHLLAGAALHIVPSERKYDLDALNDYCNQEGITISYLPTGAAEQFMQMDNQSFRVVITGGDVLKKIERNGTYKLYNGYGPTECTIMVTMFEVDKPYANIPIGKPIDRTRILILDEALALQPIGVAGELFIVGEGLGRGYLNRPELTAEKFIVHPQTGERMYRTGDRARFLPDGNIEFLGRLDNLVKIRGYRIEPGEIEPFLMNHPLIELTTVLAKEQADGRKYLVGYYVAPEEIPHGELREWLGNDLPDYMIPTYFVHMKAFPLTANGKVDRRALPDVVAPTDELEQQLAQVWSHVLGIPQMGIDDHFLERGGDSIKVMQLIHQLKNIGLSLRYDQLFTHPTIRQLKRLLTEQAAA 770
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680||     701       711       721       731       741       751       761         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  681|                                                                             
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   693                                                                             


Chain B from PDB  Type:PROTEIN  Length:768
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee.......hhhhhhhhhh..eeeee.......hhhhh...eeeee......hhhhhhhh...eeeee.......ee.hhhhhhhhh....eeeeee.........eeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhh.............eehhhhhhhhhhhh..hhhhhhhhhhhhh...........hhhhhhhhhhhhh...eeeee..eeeehhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhh...eeeehhhhhhhhh...eeee..hhhhh...............eeeeeee.......eeeeeehhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhh..eee.hhhhhhhhh........eeeee.............eeeeee.hhhhh...eeeee..........ee...eeeeee............eeeeeee.....ee..hhhhhhhheee......eeeeeeeeeee.....eee.......eee..eeehhhhhhhhhhh.....eeeeeeee.....eeeeeeee.....hhhhhhhhhhh..hhhhh..eeeee...........hhhhh................hhhhhhhhhhhhhhhh.........hhhhh.hhhhhhhhhhhhhhh....hhhhhhhh.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5es8 B   1 MGRILFLTTFMSKGNKVVRYLESLHHEVVICQEKVHAQSANLQEIDWIVSYAYGYILDKEIVSRFRGRIINLHPSLLPWNKGRDPVFWSVWDETPKGVTIHLIDEHVDTGDILVQEEIAFADEDTLLDCYNKANQAIEELFIREWENIVHGRIAPYRQTAGGTLHFKADRDFYKNLNMTTVRELLALKRLCAEPKRGEKPIDKTFHQLFEQQVEMTPDHVAVVDRGQSLTYKQLNERANQLAHHLRGKGVKPDDQVAIMLDKSLDMIVSILAVMKAGGAYVPIDPDYPGERIAYMLADSSAAILLTNALHEEKANGACDIIDVHDPDSYSENTNNLPHVNRPDDLVYVMYTSGSTGLAKGVMIEHHNLVNFCEWYRPYFGVTPADKALVYSSFSFDGSALDIFTHLLAGAALHIVPSERKYDLDALNDYCNQEGITISYLPTGAAEQFMQMDNQSFRVVITGGDVLKKIERNGTYKLYNGYGPTECTIMVTMFEVDKPYANIPIGKPIDRTRILILDEALALQPIGVAGELFIVGEGLGRGYLNRPELTAEKFIVHPQTGERMYRTGDRARFLPDGNIEFLGRLDNLVKIRGYRIEPGEIEPFLMNHPLIELTTVLAKEQADGRKYLVGYYVAPEEIPHGELREWLGNDLPDYMIPTYFVHMKAFPLTANGKVDRRALPDVQADAELLDYVAPTDELEQQLAQVWSHVLGIPQMGIDDHFLERGGDSIKVMQLIHQLKNIGLSLRYDQLFTHPTIRQLKRLLTEQAAA 770
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       692       702       712       722       732       742       752       762        
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         688|                                                                               
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          691
   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  (0, 0)

(no "SCOP Domain" information available for 5ES8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5ES8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5ES8)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

 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
    5S4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5es8)
 
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
  5es8
    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
  LGRA_BREPA | Q70LM7
    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
  LGRA_BREPA | Q70LM7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        LGRA_BREPA | Q70LM7: 5es5 5es6 5es7 5es9 5jnf

(-) Related Entries Specified in the PDB File

5es5 5ES5 CONTAINS THE SAME PROTEIN CONSTRUCT WHERE THE PEPTIDYL CARRIER PROTEIN IS DISORDERED.
5es6 5ES6 CONTAINS A SHORTER CONSTRUCT OF THE PROTEIN THAT DOES NOT INCLUDE THE PEPTIDYL CARRIER PROTEIN.
5es7 5ES7 CONTAINS A SHORTER CONSTRUCT OF THE PROTEIN THAT DOES NOT INCLUDE THE PEPTIDYL CARRIER PROTEIN AND IS SOAKED WITH SUBSTRATES.
5es9 5ES9 CONTAINS THE SAME PROTEIN, BUT IN THE FORMYLATION STATE CONFORMATION.