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 4-AMINOBUTYRATE AMINOTRANSFERASE GABT FROM MYCOBACTERIUM MARINUM COVALENTLY BOUND TO PYRIDOXAL PHOSPHATE
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  17 Mar 11  (Deposition) - 30 Mar 11  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (4x)
Keywords :  Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Mycobacterium, Tuberculosis, Smegmatis, Marinum, Water Contaminant, Pyridoxal Phosphate, Plp, Llp, Gamma Amino Butyric Acid, Gaba, Gaba Transferase, Gabaculine, Phenelzine, Aminooxyacetic Acid, Phenylethylidenehydrazine, Vigabatrin, Valproic Acid, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Baugh, I. Phan, D. W. Begley, M. C. Clifton, B. Armour, D. M. Dranow, B. M. Taylor, M. M. Muruthi, J. Abendroth, J. W. Fairman, D. Fox, S. H. Dieterich, B. L. Staker, A. S. Gardberg, R. Choi, S. N. Hewitt, A. J. Napuli, J. Myers, L. K. Barrett, Y. Zhang, M. Ferrell, E. Mundt, K. Thompkins, N. Tran, S. Lyons-Abbott, A. Abramov, A. Sekar, D. Serbzhinskiy, D. Lorimer, G. W. Buchko, R. Stacy, L. J. Stewart, T. E. Edwards, W. C. Van Voorhis, P. J. Myler
Increasing The Structural Coverage Of Tuberculosis Drug Targets.
Tuberculosis (Edinb) V. 95 142 2015
PubMed-ID: 25613812  |  Reference-DOI: 10.1016/J.TUBE.2014.12.003

(-) Compounds

Molecule 1 - 4-AMINOBUTYRATE AMINOTRANSFERASE GABT
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PAVA0421
    Gene: GABT, MMAR_2118
    Organism Scientific: MYCOBACTERIUM MARINUM
    Organism Taxid: 216594
    Strain: ATCC BAA-535 / M

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A
Biological Unit 2 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2LLP1Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
3MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4NA1Ligand/IonSODIUM ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
3MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4NA-1Ligand/IonSODIUM ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2LLP4Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
3MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4NA-1Ligand/IonSODIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:172 , ASN A:222 , ALA A:311 , HIS A:313BINDING SITE FOR RESIDUE MPD A 446
2AC2SOFTWAREMET A:94 , TYR A:153 , ARG A:156BINDING SITE FOR RESIDUE CL A 447
3AC3SOFTWARELEU A:10BINDING SITE FOR RESIDUE CL A 448
4AC4SOFTWAREARG A:352BINDING SITE FOR RESIDUE CL A 450
5AC5SOFTWAREALA A:27 , HOH A:471 , HOH A:537 , HOH A:653 , HOH A:654BINDING SITE FOR RESIDUE NA A 451

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R4T)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ile A:14 -Pro A:15
2Met A:168 -Pro A:169
3Gly A:175 -Pro A:176

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R4T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R4T)

(-) Exons   (0, 0)

(no "Exon" information available for 3R4T)

(-) 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:444
 aligned with B2HN70_MYCMM | B2HN70 from UniProtKB/TrEMBL  Length:446

    Alignment length:444
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441    
         B2HN70_MYCMM     2 ASLDQSRLLVTEIPGPASLELNKRRAAAVSGGVGVTLPVFVVRAGGGIVEDADGNRLIDLGSGIAVTTIGNSAPRVVDAVRDQVEQFTHTCFMVTPYEQYVAVAEQLNRITPGSGEKRTVLFNSGAEAVENSIKVARAHTRKQAVVAFDYAYHGRTNLTMALTAKSMPYKSGFGPFAPEIYRAPVSYPYRDNLLDKDIATDGELAAERAINLIDKQIGAANLAAVIIEPIAGEGGFIVPADGFLPALQRWCRDNDVVFIADEVQTGFARTGAMFACDHENVEPDLIVTAKGIADGFPLSAVTGRAEIMDAPHTSGLGGTFGGNPVACAAALATIETIERDGMVERARQIERLVMDRLLRLQAADDRLGDVRGRGAMIAMELVKSGTAEPDAALTQKLAAAAHAAGVIVLTCGMFGNVIRLLPPLTISDELLSEGLDILCQILAD 445
               SCOP domains d3r4ta_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---------------------------------------Aminotran_3-3r4tA01 A:41-384                                                                                                                                                                                                                                                                                                                            ------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhh...........eeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhh................eeee...hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee..............hhhhhhhhhhhhh..eeeee............hhhhhhh....eeeehhhhhh....eeeeeehhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeee........hhhhhhhhhhhhhhh.ee.eee.....eeee......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3r4t A   2 ASLDQSRLLVTEIPGPASLELNKRRAAAVSGGVGVTLPVFVVRAGGGIVEDADGNRLIDLGSGIAVTTIGNSAPRVVDAVRDQVEQFTHTCFMVTPYEQYVAVAEQLNRITPGSGEKRTVLFNSGAEAVENSIKVARAHTRKQAVVAFDYAYHGRTNLTMALTAKSMPYKSGFGPFAPEIYRAPVSYPYRDNLLDKDIATDGELAAERAINLIDKQIGAANLAAVIIEPIAGEGGFIVPADGFLPALQRWCRDNDVVFIADEVQTGFARTGAMFACDHENVEPDLIVTAkGIADGFPLSAVTGRAEIMDAPHTSGLGGTFGGNPVACAAALATIETIERDGMVERARQIERLVMDRLLRLQAADDRLGDVRGRGAMIAMELVKSGTAEPDAALTQKLAAAAHAAGVIVLTCGMFGNVIRLLPPLTISDELLSEGLDILCQILAD 445
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441    
                                                                                                                                                                                                                                                                                                                           291-LLP
   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  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R4T)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: PLP_aminotran (240)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (B2HN70_MYCMM | B2HN70)
molecular function
    GO:0003867    4-aminobutyrate transaminase activity    Catalysis of the reaction: 4-aminobutanoate + amino group acceptor = succinate semialdehyde + amino acid.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0008483    transaminase activity    Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0009448    gamma-aminobutyric acid metabolic process    The chemical reactions and pathways involving gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms.

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    LLP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MPD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:175 - Pro A:176   [ RasMol ]  
    Ile A:14 - Pro A:15   [ RasMol ]  
    Met A:168 - Pro A:169   [ RasMol ]  
 
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
  3r4t
    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
  B2HN70_MYCMM | B2HN70
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  B2HN70_MYCMM | B2HN70
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3R4T)

(-) Related Entries Specified in the PDB File

3oks SAME PROTEIN FROM MYCOBACTERIUM SMEGMATIS, FIRST GENE
3q8n SAME PROTEIN FROM MYCOBACTERIUM SMEGMATIS, SECOND GENE RELATED ID: MYMAA.01026.B RELATED DB: TARGETDB