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(-) Description

Title :  CRYSTAL STRUCTURE OF SHORT-CHAIN DEHYDROGENASE/REDUCTASE SDR FROM MYCOBACTERIUM SMEGMATIS
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  10 Nov 10  (Deposition) - 24 Nov 10  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (2x)
Biol. Unit 2:  B,D  (2x)
Keywords :  Ssgcid, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Oxidoreductase (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 - SHORT-CHAIN DEHYDROGENASE/REDUCTASE SDR
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MSMEG_0779
    Organism Scientific: MYCOBACTERIUM SMEGMATIS
    Organism Taxid: 246196
    Strain: ATCC 700084 / MC(2)155

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 18)

Asymmetric Unit (4, 18)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
2CL4Ligand/IonCHLORIDE ION
3GOL7Ligand/IonGLYCEROL
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3GOL6Ligand/IonGLYCEROL
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3GOL8Ligand/IonGLYCEROL
4PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:95 , TRP A:154 , HOH A:340 , HOH A:870BINDING SITE FOR RESIDUE PEG A 265
02AC2SOFTWAREASP A:97 , HOH A:291 , HOH A:598 , ASP C:97 , HOH C:302BINDING SITE FOR RESIDUE CA A 270
03AC3SOFTWARELEU A:165 , ARG A:169 , CL C:275BINDING SITE FOR RESIDUE CL A 275
04AC4SOFTWAREASP A:51 , GLY A:54 , GLY A:56 , HOH A:283 , HOH A:319BINDING SITE FOR RESIDUE CA A 280
05AC5SOFTWAREASN A:91 , GLY A:93 , THR A:141 , TYR A:157 , LYS A:161BINDING SITE FOR RESIDUE GOL A 285
06AC6SOFTWARETYR B:151 , HOH B:341 , HOH B:467 , HOH B:879BINDING SITE FOR RESIDUE GOL B 267
07AC7SOFTWAREASP B:97 , HOH B:291 , HOH B:331 , HOH B:772 , ASP D:97 , HOH D:327 , HOH D:658BINDING SITE FOR RESIDUE CA B 270
08AC8SOFTWAREARG B:169 , CL D:275BINDING SITE FOR RESIDUE CL B 275
09AC9SOFTWAREASP B:51 , GLY B:54 , GLY B:56 , HOH B:319 , HOH B:431BINDING SITE FOR RESIDUE CA B 280
10BC1SOFTWAREASN B:91 , ALA B:92 , GLY B:93 , THR B:141 , TYR B:157 , LYS B:161 , HOH B:296BINDING SITE FOR RESIDUE GOL B 285
11BC2SOFTWAREHOH C:889BINDING SITE FOR RESIDUE GOL C 267
12BC3SOFTWARECL A:275 , ARG C:169BINDING SITE FOR RESIDUE CL C 275
13BC4SOFTWAREASP C:51 , GLY C:54 , GLY C:56 , HOH C:311 , HOH C:532BINDING SITE FOR RESIDUE CA C 280
14BC5SOFTWAREASN C:91 , ALA C:92 , GLY C:93 , THR C:141 , TYR C:157 , LYS C:161 , HOH C:330BINDING SITE FOR RESIDUE GOL C 285
15BC6SOFTWAREHOH D:514 , HOH D:828 , HOH D:903BINDING SITE FOR RESIDUE GOL D 267
16BC7SOFTWARECL B:275 , LEU D:165 , ARG D:169BINDING SITE FOR RESIDUE CL D 275
17BC8SOFTWAREPRO C:-2 , HOH C:509 , ASP D:51 , GLY D:54 , GLY D:56 , HOH D:315BINDING SITE FOR RESIDUE CA D 280
18BC9SOFTWAREASN D:91 , ALA D:92 , GLY D:93 , THR D:141 , TYR D:157 , LYS D:161 , HOH D:344BINDING SITE FOR RESIDUE GOL D 285

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PK0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3PK0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PK0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PK0)

(-) Exons   (0, 0)

(no "Exon" information available for 3PK0)

(-) 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:260
 aligned with A0QQJ6_MYCS2 | A0QQJ6 from UniProtKB/TrEMBL  Length:258

    Alignment length:260
                              1                                                                                                                                                                                                                                                                 
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258
         A0QQJ6_MYCS2     - --MFDLQGRSVVVTGGTKGIGRGIATVFARAGANVAVAGRSTADIDACVADLDQLGSGKVIGVQTDVSDRAQCDALAGRAVEEFGGIDVVCANAGVFPDAPLATMTPEQLNGIFAVNVNGTFYAVQACLDALIASGSGRVVLTSSITGPITGYPGWSHYGATKAAQLGFMRTAAIELAPHKITVNAIMPGNIMTEGLLENGEEYIASMARSIPAGALGTPEDIGHLAAFLATKEAGYITGQAIAVDGGQVLPESLDAIAT 258
               SCOP domains d3pk0a_ A: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee............hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhh.hhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee........hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pk0 A  -1 GSMFDLQGRSVVVTGGTKGIGRGIATVFARAGANVAVAGRSTADIDACVADLDQLGSGKVIGVQTDVSDRAQCDALAGRAVEEFGGIDVVCANAGVFPDAPLATMTPEQLNGIFAVNVNGTFYAVQACLDALIASGSGRVVLTSSITGPITGYPGWSHYGATKAAQLGFMRTAAIELAPHKITVNAIMPGNIMTEGLLENGEEYIASMARSIPAGALGTPEDIGHLAAFLATKEAGYITGQAIAVDGGQVLPESLDAIAT 258
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258


Chain B from PDB  Type:PROTEIN  Length:262
 aligned with A0QQJ6_MYCS2 | A0QQJ6 from UniProtKB/TrEMBL  Length:258

    Alignment length:262
                                1                                                                                                                                                                                                                                                                 
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256  
         A0QQJ6_MYCS2     - ----MFDLQGRSVVVTGGTKGIGRGIATVFARAGANVAVAGRSTADIDACVADLDQLGSGKVIGVQTDVSDRAQCDALAGRAVEEFGGIDVVCANAGVFPDAPLATMTPEQLNGIFAVNVNGTFYAVQACLDALIASGSGRVVLTSSITGPITGYPGWSHYGATKAAQLGFMRTAAIELAPHKITVNAIMPGNIMTEGLLENGEEYIASMARSIPAGALGTPEDIGHLAAFLATKEAGYITGQAIAVDGGQVLPESLDAIAT 258
               SCOP domains d3pk0b_ B: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee............hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhh.hhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee........hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pk0 B  -3 GPGSMFDLQGRSVVVTGGTKGIGRGIATVFARAGANVAVAGRSTADIDACVADLDQLGSGKVIGVQTDVSDRAQCDALAGRAVEEFGGIDVVCANAGVFPDAPLATMTPEQLNGIFAVNVNGTFYAVQACLDALIASGSGRVVLTSSITGPITGYPGWSHYGATKAAQLGFMRTAAIELAPHKITVNAIMPGNIMTEGLLENGEEYIASMARSIPAGALGTPEDIGHLAAFLATKEAGYITGQAIAVDGGQVLPESLDAIAT 258
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256  


Chain C from PDB  Type:PROTEIN  Length:262
 aligned with A0QQJ6_MYCS2 | A0QQJ6 from UniProtKB/TrEMBL  Length:258

    Alignment length:262
                                1                                                                                                                                                                                                                                                                 
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256  
         A0QQJ6_MYCS2     - ----MFDLQGRSVVVTGGTKGIGRGIATVFARAGANVAVAGRSTADIDACVADLDQLGSGKVIGVQTDVSDRAQCDALAGRAVEEFGGIDVVCANAGVFPDAPLATMTPEQLNGIFAVNVNGTFYAVQACLDALIASGSGRVVLTSSITGPITGYPGWSHYGATKAAQLGFMRTAAIELAPHKITVNAIMPGNIMTEGLLENGEEYIASMARSIPAGALGTPEDIGHLAAFLATKEAGYITGQAIAVDGGQVLPESLDAIAT 258
               SCOP domains d3pk0c_ C: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee............hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhh.hhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee........hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pk0 C  -3 GPGSMFDLQGRSVVVTGGTKGIGRGIATVFARAGANVAVAGRSTADIDACVADLDQLGSGKVIGVQTDVSDRAQCDALAGRAVEEFGGIDVVCANAGVFPDAPLATMTPEQLNGIFAVNVNGTFYAVQACLDALIASGSGRVVLTSSITGPITGYPGWSHYGATKAAQLGFMRTAAIELAPHKITVNAIMPGNIMTEGLLENGEEYIASMARSIPAGALGTPEDIGHLAAFLATKEAGYITGQAIAVDGGQVLPESLDAIAT 258
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256  


Chain D from PDB  Type:PROTEIN  Length:259
 aligned with A0QQJ6_MYCS2 | A0QQJ6 from UniProtKB/TrEMBL  Length:258

    Alignment length:259
                             1                                                                                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249         
         A0QQJ6_MYCS2     - -MFDLQGRSVVVTGGTKGIGRGIATVFARAGANVAVAGRSTADIDACVADLDQLGSGKVIGVQTDVSDRAQCDALAGRAVEEFGGIDVVCANAGVFPDAPLATMTPEQLNGIFAVNVNGTFYAVQACLDALIASGSGRVVLTSSITGPITGYPGWSHYGATKAAQLGFMRTAAIELAPHKITVNAIMPGNIMTEGLLENGEEYIASMARSIPAGALGTPEDIGHLAAFLATKEAGYITGQAIAVDGGQVLPESLDAIAT 258
               SCOP domains d3pk0d_ D: automated matches                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------adh_short-3pk0D01 D:7-176                                                                                                                                                 ---------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------adh_short-3pk0D02 D:7-176                                                                                                                                                 ---------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -------adh_short-3pk0D03 D:7-176                                                                                                                                                 ---------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -------adh_short-3pk0D04 D:7-176                                                                                                                                                 ---------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ........eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee............hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee........hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pk0 D   0 SMFDLQGRSVVVTGGTKGIGRGIATVFARAGANVAVAGRSTADIDACVADLDQLGSGKVIGVQTDVSDRAQCDALAGRAVEEFGGIDVVCANAGVFPDAPLATMTPEQLNGIFAVNVNGTFYAVQACLDALIASGSGRVVLTSSITGPITGYPGWSHYGATKAAQLGFMRTAAIELAPHKITVNAIMPGNIMTEGLLENGEEYIASMARSIPAGALGTPEDIGHLAAFLATKEAGYITGQAIAVDGGQVLPESLDAIAT 258
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PK0)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (A0QQJ6_MYCS2 | A0QQJ6)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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