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(-) Description

Title :  CRYSTAL STRUCTURE OF DECAPLANIN - SPACE GROUP P21, SECOND FORM
 
Authors :  C. Lehmann, L. Vertesy, G. M. Sheldrick, Z. Dauter, M. Dauter
Date :  22 Dec 00  (Deposition) - 11 Jul 05  (Release) - 01 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.13
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Antibiotic, Glycopeptide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Lehmann, J. E. Debreczeni, G. Bunkoczi, M. Dauter, Z. Dauter, L. Vertesy, G. M. Sheldrick
Structures Of Four Crystal Forms Of Decaplanin
Helv. Chim. Acta V. 86 1478 2003
PubMed: search  |  Reference-DOI: 10.1002/HLCA.200390131

(-) Compounds

Molecule 1 - DECAPLANIN
    Chains: A, B, C, D
    Organism Scientific: UNCULTURED ACTINOMYCETE
    Organism Taxid: 100235
    Other Details: CULTURE HIL Y-86, 36910
    Strain: DSM 4763
    Synonym: M86-1410

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 39)

Asymmetric Unit (9, 39)
No.NameCountTypeFull Name
13FG4Mod. Amino Acid(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID
2BGC4Ligand/IonBETA-D-GLUCOSE
3CIT3Ligand/IonCITRIC ACID
4ERE4Ligand/Ion(1R,3S,4R,5S)-3-AMINO-2,3,6-TRIDEOXY-3-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSE
5GHP8Mod. Amino Acid(2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC ACID
6MLU4Mod. Amino AcidN-METHYL-D-LEUCINE
7OMX4Mod. Amino Acid(BETAR)-BETA-HYDROXY-L-TYROSINE
8OMZ4Mod. Amino Acid(BETAR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE
9RAM4Ligand/IonALPHA-L-RHAMNOSE
Biological Unit 1 (9, 19)
No.NameCountTypeFull Name
13FG2Mod. Amino Acid(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID
2BGC2Ligand/IonBETA-D-GLUCOSE
3CIT1Ligand/IonCITRIC ACID
4ERE2Ligand/Ion(1R,3S,4R,5S)-3-AMINO-2,3,6-TRIDEOXY-3-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSE
5GHP4Mod. Amino Acid(2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC ACID
6MLU2Mod. Amino AcidN-METHYL-D-LEUCINE
7OMX2Mod. Amino Acid(BETAR)-BETA-HYDROXY-L-TYROSINE
8OMZ2Mod. Amino Acid(BETAR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE
9RAM2Ligand/IonALPHA-L-RHAMNOSE
Biological Unit 2 (9, 20)
No.NameCountTypeFull Name
13FG2Mod. Amino Acid(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID
2BGC2Ligand/IonBETA-D-GLUCOSE
3CIT2Ligand/IonCITRIC ACID
4ERE2Ligand/Ion(1R,3S,4R,5S)-3-AMINO-2,3,6-TRIDEOXY-3-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSE
5GHP4Mod. Amino Acid(2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC ACID
6MLU2Mod. Amino AcidN-METHYL-D-LEUCINE
7OMX2Mod. Amino Acid(BETAR)-BETA-HYDROXY-L-TYROSINE
8OMZ2Mod. Amino Acid(BETAR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE
9RAM2Ligand/IonALPHA-L-RHAMNOSE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN B:3 , GHP B:5 , 3FG B:7 , HOH B:2023 , MLU D:1 , OMZ D:2 , ASN D:3 , GHP D:4 , HOH D:2037 , HOH D:2038 , HOH D:2042BINDING SITE FOR RESIDUE CIT D1001
2AC2SOFTWAREMLU A:1 , OMZ A:2 , ASN A:3 , GHP A:4 , HOH A:2037BINDING SITE FOR RESIDUE CIT A1002
3AC3SOFTWAREMLU C:1 , OMZ C:2 , ASN C:3 , GHP C:4BINDING SITE FOR RESIDUE CIT C1003
4AC4SOFTWARECIT A:1002 , HOH A:2004 , HOH A:2005 , HOH A:2006 , HOH A:2014 , HOH A:2015 , HOH A:2016 , HOH A:2017 , HOH A:2018 , HOH A:2020 , HOH A:2021 , HOH A:2022 , HOH A:2023 , HOH A:2037 , OMZ B:2 , ASN B:3 , GHP B:4 , GHP B:5 , OMX B:6 , HOH B:2027BINDING SITE FOR CHAIN A OF DECAPLANIN
5AC5SOFTWAREOMZ A:2 , ASN A:3 , GHP A:4 , GHP A:5 , OMX A:6 , HOH B:2001 , HOH B:2002 , HOH B:2008 , HOH B:2009 , HOH B:2010 , HOH B:2022 , HOH B:2023 , HOH B:2025 , HOH B:2026 , HOH B:2027 , HOH B:2028 , HOH B:2029 , HOH B:2030 , OMX D:6 , 3FG D:7 , CIT D:1001 , HOH D:2022 , HOH D:2023 , HOH D:2042BINDING SITE FOR CHAIN B OF DECAPLANIN
6AC6SOFTWARECIT C:1003 , HOH C:2004 , HOH C:2005 , HOH C:2013 , HOH C:2016 , HOH C:2024 , HOH C:2025 , HOH C:2027 , HOH C:2028 , HOH C:2029 , HOH C:2030 , HOH C:2035 , OMZ D:2 , ASN D:3 , GHP D:4 , GHP D:5 , OMX D:6BINDING SITE FOR CHAIN C OF DECAPLANIN
7AC7SOFTWAREOMX B:6 , 3FG B:7 , HOH B:2028 , OMZ C:2 , ASN C:3 , GHP C:4 , GHP C:5 , OMX C:6 , HOH C:2025 , CIT D:1001 , HOH D:2003 , HOH D:2008 , HOH D:2009 , HOH D:2016 , HOH D:2017 , HOH D:2018 , HOH D:2020 , HOH D:2021 , HOH D:2022 , HOH D:2023 , HOH D:2025BINDING SITE FOR CHAIN D OF DECAPLANIN

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1HHC)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ghp A:5 -Omx A:6
2Ghp B:5 -Omx B:6
3Ghp C:5 -Omx C:6
4Ghp D:5 -Omx D:6

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1HHC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1HHC)

(-) Exons   (0, 0)

(no "Exon" information available for 1HHC)

(-) 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:7
                                     
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                   1hhc A 1 xxNxxxx 7
                            || ||||
                            || ||||
                            1-MLU||
                             2-OMZ|
                               4-GHP
                                5-GHP
                                 6-OMX
                                  7-3FG


Chain B from PDB  Type:PROTEIN  Length:7
                                     
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                   1hhc B 1 xxNxxxx 7
                            || ||||
                            || ||||
                            1-MLU||
                             2-OMZ|
                               4-GHP
                                5-GHP
                                 6-OMX
                                  7-3FG


Chain C from PDB  Type:PROTEIN  Length:7
                                     
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                   1hhc C 1 xxNxxxx 7
                            || ||||
                            || ||||
                            1-MLU||
                             2-OMZ|
                               4-GHP
                                5-GHP
                                 6-OMX
                                  7-3FG


Chain D from PDB  Type:PROTEIN  Length:7
                                     
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                   1hhc D 1 xxNxxxx 7
                            || ||||
                            || ||||
                            1-MLU||
                             2-OMZ|
                               4-GHP
                                5-GHP
                                 6-OMX
                                  7-3FG
   Legend:   → Mismatch (orange background)
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    → 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 1HHC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1HHC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HHC)

(-) Gene Ontology  (0, 0)

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(-) Related Entries Specified in the PDB File

1hh3 CRYSTAL STRUCTURE OF DECAPLANIN - SPACE GROUP P21
1hha CRYSTAL STRUCTURE OF DECAPLANIN - SPACE GROUP P6122
1hhf CRYSTAL STRUCTURE OF DECAPLANIN - SPACE GROUP P6122, SECOND FORM