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(-) Description

Title :  CRYSTAL STRUCTURE OF SLGN1DELTAASUB IN COMPLEX WITH AMPCPP
 
Authors :  D. A. Herbst, G. Zocher, T. Stehle
Date :  24 Aug 12  (Deposition) - 28 Nov 12  (Release) - 06 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Mbth-Like Domain, Adenylation Domain, Ligase, Rossmann Fold, Atp Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. A. Herbst, B. Boll, G. Zocher, T. Stehle, L. Heide
Structural Basis Of The Interaction Of Mbth-Like Proteins, Putative Regulators Of Nonribosomal Peptide Biosynthesis, With Adenylating Enzymes.
J. Biol. Chem. V. 288 1991 2013
PubMed-ID: 23192349  |  Reference-DOI: 10.1074/JBC.M112.420182

(-) Compounds

Molecule 1 - NON-RIBOSOMAL PEPTIDE SYNTHETASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3) YBDZ-
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SLGN1
    Organism Scientific: STREPTOMYCES LYDICUS
    Organism Taxid: 47763

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1APC4Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2CL1Ligand/IonCHLORIDE ION
3TLA6Ligand/IonL(+)-TARTARIC ACID
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1APC1Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2CL-1Ligand/IonCHLORIDE ION
3TLA1Ligand/IonL(+)-TARTARIC ACID
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1APC1Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2CL-1Ligand/IonCHLORIDE ION
3TLA2Ligand/IonL(+)-TARTARIC ACID
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1APC1Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2CL-1Ligand/IonCHLORIDE ION
3TLA1Ligand/IonL(+)-TARTARIC ACID
Biological Unit 4 (2, 3)
No.NameCountTypeFull Name
1APC1Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2CL-1Ligand/IonCHLORIDE ION
3TLA2Ligand/IonL(+)-TARTARIC ACID

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:227 , TRP A:262 , GLY A:332 , GLU A:333 , PRO A:334 , ASN A:354 , GLY A:355 , TYR A:356 , GLY A:357 , PRO A:358 , ALA A:359 , GLU A:360 , ASP A:449 , TYR A:461 , ARG A:464 , HOH A:701 , HOH A:702 , HOH A:703 , HOH A:723 , HOH A:789 , HOH A:829 , HOH A:844 , HOH A:890 , HOH A:893 , HOH A:923BINDING SITE FOR RESIDUE APC A 601
02AC2SOFTWAREARG A:21 , ARG A:234 , GLY A:413 , ALA A:414 , LEU A:416 , ARG A:443 , HOH A:716BINDING SITE FOR RESIDUE TLA A 602
03AC3SOFTWAREPRO A:86 , ASP A:87 , HOH A:1006BINDING SITE FOR RESIDUE CL A 603
04AC4SOFTWARELYS B:227 , TRP B:262 , GLY B:332 , GLU B:333 , PRO B:334 , ASN B:354 , GLY B:355 , TYR B:356 , GLY B:357 , PRO B:358 , ALA B:359 , GLU B:360 , ASP B:449 , TYR B:461 , ARG B:464 , HOH B:701 , HOH B:702 , HOH B:703 , HOH B:738 , HOH B:791 , HOH B:817 , HOH B:880 , HOH B:882 , HOH B:903 , HOH B:910 , HOH B:919 , HOH B:933BINDING SITE FOR RESIDUE APC B 601
05AC5SOFTWAREGLU B:52 , ARG B:225 , SER B:422 , ARG B:423 , PRO B:424 , ALA B:425 , LEU B:426BINDING SITE FOR RESIDUE TLA B 602
06AC6SOFTWAREARG B:21 , ARG B:234 , GLY B:413 , ALA B:414 , GLU B:442 , ARG B:443 , HOH B:735BINDING SITE FOR RESIDUE TLA B 603
07AC7SOFTWARELYS C:227 , TRP C:262 , GLY C:332 , GLU C:333 , PRO C:334 , ASN C:354 , GLY C:355 , TYR C:356 , GLY C:357 , PRO C:358 , ALA C:359 , GLU C:360 , ASP C:449 , TYR C:461 , ARG C:464 , HOH C:706 , HOH C:707 , HOH C:708 , HOH C:752 , HOH C:773 , HOH C:828 , HOH C:829BINDING SITE FOR RESIDUE APC C 601
08AC8SOFTWAREARG C:21 , ARG C:234 , GLY C:413 , ALA C:414 , GLU C:442 , ARG C:443 , HOH C:836BINDING SITE FOR RESIDUE TLA C 602
09AC9SOFTWARELYS D:227 , TRP D:262 , GLY D:332 , GLU D:333 , PRO D:334 , ASN D:354 , GLY D:355 , TYR D:356 , GLY D:357 , PRO D:358 , ALA D:359 , GLU D:360 , ASP D:449 , TYR D:461 , ARG D:464 , HOH D:1032 , HOH D:1036 , HOH D:1037 , HOH D:1038 , HOH D:1054 , HOH D:1116 , HOH D:1120 , HOH D:1127 , HOH D:1241 , HOH D:1262BINDING SITE FOR RESIDUE APC D 601
10BC1SOFTWAREGLU D:52 , ARG D:225 , ARG D:423 , PRO D:424 , ALA D:425 , LEU D:426BINDING SITE FOR RESIDUE TLA D 602
11BC2SOFTWAREARG D:21 , ARG D:234 , GLY D:413 , ALA D:414 , GLU D:442 , ARG D:443 , HOH D:1125BINDING SITE FOR RESIDUE TLA D 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GR5)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Gly A:40 -Thr A:41
2Gly B:40 -Thr B:41
3Gly B:62 -Pro B:63
4Gly C:40 -Thr C:41
5Gly D:40 -Thr D:41

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GR5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GR5)

(-) Exons   (0, 0)

(no "Exon" information available for 4GR5)

(-) 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:451
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee.....eeeee.........eeeeeeehhhhhhhhhhhhh............hhhhhhhhhhhhh...eeeee..eeeehhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh..eeee...........eeee...............eeeee...........eeeehhhhhhhhh...........eeee.......hhhhhhhhhhh...eeee......hhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhh...eeeeee.hhhhh...eeee.hhhhh........ee...eeeeee...........eeeeeeee.....ee..hhhhhhhheee.........eeeeeeeeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gr5 A   2 SNPFEEYDGGHVVLTDALGRHSLWPAGIAVPAGWSVRHGTDSREGCLAHIEHHWTDLRPTRAPAGACVHELFEAQAARAPDAVALLHEADELTYGALNERANRLAHRLVGLGVAPGTLVGVHLERGFDMVVALLAVLKAGGGYTMLDPQFPVERLALSLEDTGAPLLVTSRPLSGRLTGTTTLYVEDAGNLATGVGPEDVACVMFTSGSTGRPKGVMSPHRALTGTYLGQDYAGFGPDEVFLQCSPVSWDAFGLELFGALLFGARCVLQSGQNPDPLEIGELVARHGVTMLQLSASLFNFLVDEVPEAFEGVRYAITGGEPASVPHVAKARRDHPALRLGNGYGPAESMGFTTHHAVVAGDLSGTALPIGVPLAGKRAYVLDDDLKPAANGALGELYVAGAGLAHGYVSRPALTAERFVADPFAGPGGERMYRTGDLARRRADGVLEYVGR 464
                                    11        21        31        41        51        61|       76        86        96       106       116       126       136       146       156       166       176       186      |203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463 
                                                                                      61|                                                                                                                           193|                                                                                                                                                                                                                                                                       
                                                                                       67                                                                                                                            201                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:455
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee.....eeeee.........eeeeeeehhhhhhhhhhhhh..........hhhhhhhhhhhhh...eeeee..eeeehhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh..eeee...........eeee...................eeeee...........eeeehhhhhhhhh...........eeee.......hhhhhhhhhhh...eeee......hhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhh...eeeeee.hhhhh...eeee.hhhhhhh......ee...eeeeee............eeeeeee.....ee..hhhhhhhheee.........eeeeeeeeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gr5 B   0 HMSNPFEEYDGGHVVLTDALGRHSLWPAGIAVPAGWSVRHGTDSREGCLAHIEHHWTDLRPTGPGACVHELFEAQAARAPDAVALLHEADELTYGALNERANRLAHRLVGLGVAPGTLVGVHLERGFDMVVALLAVLKAGGGYTMLDPQFPVERLALSLEDTGAPLLVTSRPLSGRLTGTTTLYVEDSDAPAGNLATGVGPEDVACVMFTSGSTGRPKGVMSPHRALTGTYLGQDYAGFGPDEVFLQCSPVSWDAFGLELFGALLFGARCVLQSGQNPDPLEIGELVARHGVTMLQLSASLFNFLVDEVPEAFEGVRYAITGGEPASVPHVAKARRDHPALRLGNGYGPAESMGFTTHHAVVAGDLSGTALPIGVPLAGKRAYVLDDDLKPAANGALGELYVAGAGLAHGYVSRPALTAERFVADPFAGPGGERMYRTGDLARRRADGVLEYVGR 464
                                     9        19        29        39        49        59   ||   76        86        96       106       116       126       136       146       156       166       176       186      |199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459     
                                                                                          63|                                                                                                                       193|                                                                                                                                                                                                                                                                           
                                                                                           71                                                                                                                        197                                                                                                                                                                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:457
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee.....eeeee.........eeeeeeehhhhhhhhhhhhh........hhhhh....hhhhhhhhhhhhh...eeeee..eeeehhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh..eeee.hhhh......eeee................eeeee...........eeeehhhhhhhhh...........eeee.......hhhhhhhhhhh...eeee......hhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhh...eeeeee.hhhhh...eeee.hhhhhh.......ee...eeeeee............eeeeeee.....ee..hhhhhhhheee.........eeeeeeeeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gr5 C   2 SNPFEEYDGGHVVLTDALGRHSLWPAGIAVPAGWSVRHGTDSREGCLAHIEHHWTDLRPTGPAVERAPAGACVHELFEAQAARAPDAVALLHEADELTYGALNERANRLAHRLVGLGVAPGTLVGVHLERGFDMVVALLAVLKAGGGYTMLDPQFPVERLALSLEDTGAPLLVTSRPLSGRLTGTTTLYVEDPAGNLATGVGPEDVACVMFTSGSTGRPKGVMSPHRALTGTYLGQDYAGFGPDEVFLQCSPVSWDAFGLELFGALLFGARCVLQSGQNPDPLEIGELVARHGVTMLQLSASLFNFLVDEVPEAFEGVRYAITGGEPASVPHVAKARRDHPALRLGNGYGPAESMGFTTHHAVVAGDLSGTALPIGVPLAGKRAYVLDDDLKPAANGALGELYVAGAGLAHGYVSRPALTAERFVADPFAGPGGERMYRTGDLARRRADGVLEYVGR 464
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191 ||    207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       
                                                                                                                                                                                                                         193|                                                                                                                                                                                                                                                                        
                                                                                                                                                                                                                          200                                                                                                                                                                                                                                                                        


Chain D from PDB  Type:PROTEIN  Length:449
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee.....eeeee.........eeeeeeehhhhhhhhhhhhh...........hhhhhhhhhhhhh...eeeee..eeeehhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh..eeee...........eeee...............eeeee...........eeeehhhhhhhhh...........eeee.......hhhhhhhhhhh...eeee......hhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhh...eeeeee.hhhhh...eeee.hhhhhhh......ee...eeeeee............eeeeeee.....ee..hhhhhhhheee.........eeeeeeeeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gr5 D   3 NPFEEYDGGHVVLTDALGRHSLWPAGIAVPAGWSVRHGTDSREGCLAHIEHHWTDLRPTAPAGACVHELFEAQAARAPDAVALLHEADELTYGALNERANRLAHRLVGLGVAPGTLVGVHLERGFDMVVALLAVLKAGGGYTMLDPQFPVERLALSLEDTGAPLLVTSRPLSGRLTGTTTLYVEDAGNLATGVGPEDVACVMFTSGSTGRPKGVMSPHRALTGTYLGQDYAGFGPDEVFLQCSPVSWDAFGLELFGALLFGARCVLQSGQNPDPLEIGELVARHGVTMLQLSASLFNFLVDEVPEAFEGVRYAITGGEPASVPHVAKARRDHPALRLGNGYGPAESMGFTTHHAVVAGDLSGTALPIGVPLAGKRAYVLDDDLKPAANGALGELYVAGAGLAHGYVSRPALTAERFVADPFAGPGGERMYRTGDLARRRADGVLEYVGR 464
                                    12        22        32        42        52        68        78        88        98       108       118       128       138       148       158       168       178       188    || 205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455         
                                                                                     61|                                                                                                                          193|                                                                                                                                                                                                                                                                       
                                                                                      68                                                                                                                           201
   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 4GR5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GR5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GR5)

(-) Gene Ontology  (6, 6)

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        D1GLU5_9ACTN | D1GLU5: 4gr4

(-) Related Entries Specified in the PDB File

4gr4