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(-) Description

Title :  CRYSTAL STRUCTURE OF T4 LYSOZYME-PEPTIDE IN COMPLEX WITH TEICOPLANIN-A2-2
 
Authors :  S. Han, B. V. Le, H. Hajare, R. H. G. Baxter, S. J. Miller
Date :  13 May 14  (Deposition) - 10 Sep 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Site-Selective Catalyst, Carrier Protein Approach, Glycopeptide Antibiotic, Hydrolase-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Han, B. V. Le, H. S. Hajare, R. H. Baxter, S. J. Miller
X-Ray Crystal Structure Of Teicoplanin A2-2 Bound To A Catalytic Peptide Sequence Via The Carrier Protein Strategy
J. Org. Chem. V. 79 8550 2014
PubMed-ID: 25147913  |  Reference-DOI: 10.1021/JO501625F

(-) Compounds

Molecule 1 - TEICOPLANIN-A2-2
    Chains: B
    Organism Scientific: ACTINOPLANES TEICHOMYCETICUS
    Organism Taxid: 1867
 
Molecule 2 - LYSOZYME
    Chains: A
    EC Number: 3.2.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTXB1
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: E, T4TP126
    Mutation: YES
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665
    Other Details: C-TERMINAL FUSED BY MODIFIED CYS-ALA-MHS-D-PRO-AIB-D- ALA-D-ALA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (17, 21)

Asymmetric/Biological Unit (17, 21)
No.NameCountTypeFull Name
13FG2OTHER(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID
23MY1OTHER3-CHLORO-D-TYROSINE
3AIB1Mod. Amino AcidALPHA-AMINOISOBUTYRIC ACID
4CCS1Mod. Amino AcidCARBOXYMETHYLATED CYSTEINE
5CL1Ligand/IonCHLORIDE ION
6DAL2Mod. Amino AcidD-ALANINE
7DPR1Mod. Amino AcidD-PROLINE
8GCS1Ligand/IonD-GLUCOSAMINE
9GHP3OTHER(2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC ACID
10GOL1Ligand/IonGLYCEROL
11MAN1Ligand/IonALPHA-D-MANNOSE
12MHS1Mod. Amino AcidN1-METHYLATED HISTIDINE
13NA1Ligand/IonSODIUM ION
14NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
15OMY1OTHER(BETAR)-3-CHLORO-BETA-HYDROXY-L-TYROSINE
16PO41Ligand/IonPHOSPHATE ION
17T551Ligand/Ion8-METHYLNONANOIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:76 , ARG A:80binding site for residue CL A 202
2AC2SOFTWARELYS A:16 , PO4 A:204binding site for residue NA A 203
3AC3SOFTWARELYS A:16 , ARG A:137 , NA A:203 , HOH A:306 , HOH A:355 , HOH A:371 , 3FG B:3binding site for residue PO4 A 204
4AC4SOFTWAREGLU A:22 , GLN A:105 , MET A:106 , TRP A:138 , GLN A:141 , GHP B:1binding site for residue GOL A 205
5AD3SOFTWAREARG A:8 , ILE A:9 , ASP A:10 , GLU A:11 , GLY A:12 , LEU A:13 , ARG A:14 , LEU A:15 , LYS A:16 , TYR A:18 , GLU A:22 , GLY A:23 , TYR A:24 , LYS A:35 , GLU A:45 , LYS A:48 , LYS A:60 , GLU A:64 , ARG A:137 , GLN A:141 , ALA A:166 , DPR A:168 , AIB A:169 , DAL A:170 , DAL A:171 , PO4 A:204 , GOL A:205 , HOH A:371 , HOH B:201 , HOH B:202 , HOH B:204 , HOH B:205 , HOH B:206 , HOH B:207 , HOH B:208 , HOH B:209 , HOH B:210binding site for TEICOPLANIN-A2-2 chain B

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PK0)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ghp B:5 -Omy B:6

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PK0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PK0)

(-) Exons   (0, 0)

(no "Exon" information available for 4PK0)

(-) 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:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhheeeeeee.....eeee..eeee...hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhh.......ee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pk0 A   1 MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNLxAhxxxx 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    | |170|
                                                                                                                                                                                              165-CCS||
                                                                                                                                                                                                167-MHS
                                                                                                                                                                                                 168-DPR
                                                                                                                                                                                                  169-AIB
                                                                                                                                                                                                   170-DAL
                                                                                                                                                                                                    171-DAL


Chain B from PDB  Type:OTHER  Length:7
                                       
                 4pk0 B   1 xxxxxxx   7
                            |||||||
                            |||||||
                            1-GHP||
                             2-3MY|
                              3-3FG
                               4-GHP
                                5-GHP
                                 6-OMY
                                  7-3FG
   Legend:   → Mismatch (orange background)
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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 4PK0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PK0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PK0)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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  3.2.1.17
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 Related Entries

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

UniProtKB/Swiss-Prot
        D9IEF7_BPT4 | D9IEF7: 4s0w 5ndd 5ndz 5t1a 5v83 5v86 5v88 5vba 5xez 5xf1
UniProtKB/TrEMBL
        D9IEF7_BPT4 | D9IEF7: 4pjz 4pla 4qkx 4u15 4u16 4uis 4xsj 4yc4 5bz6 5i0n

(-) Related Entries Specified in the PDB File

4pjz 4PJZ CONTAINS THE SAME PROTEIN BUT WITH THREE ADDITIONAL RESIDUES IN THE LINKER REGION