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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE SHORT CHAIN DEHYDROGENASE OR REDUCTASE FROM MYCOBACTERIUM ABSCESSUS
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  13 Apr 11  (Deposition) - 20 Apr 11  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Tuberculosis, Water Contaminant, Putative Uncharacterized Protein, Potassium Ion, 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 OR REDUCTASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PAVA0421
    Gene: MAB_0952
    Organism Scientific: MYCOBACTERIUM ABSCESSUS
    Organism Taxid: 561007
    Strain: ATCC 19977 / DSM 44196

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 27)

Asymmetric/Biological Unit (3, 27)
No.NameCountTypeFull Name
1EDO19Ligand/Ion1,2-ETHANEDIOL
2K4Ligand/IonPOTASSIUM ION
3PG54Ligand/Ion1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE

(-) Sites  (27, 27)

Asymmetric Unit (27, 27)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:64 , GLY A:67 , GLY A:69 , HOH A:324 , HOH A:367 , HOH A:498BINDING SITE FOR RESIDUE K A 272
02AC2SOFTWAREPHE A:108 , TYR A:164 , TYR A:170 , HOH A:802BINDING SITE FOR RESIDUE PG5 A 273
03AC3SOFTWAREARG A:182 , HOH A:618 , ALA B:175 , ARG B:182 , HOH B:615BINDING SITE FOR RESIDUE EDO A 274
04AC4SOFTWAREASP A:114 , MET A:116BINDING SITE FOR RESIDUE EDO A 275
05AC5SOFTWAREARG A:89 , ALA A:138 , ARG B:54BINDING SITE FOR RESIDUE EDO A 276
06AC6SOFTWAREVAL A:261 , HOH A:807 , HOH A:808 , VAL D:261BINDING SITE FOR RESIDUE EDO A 277
07AC7SOFTWAREPRO A:81 , TYR A:134 , GLN A:137 , HOH A:519 , HOH A:520BINDING SITE FOR RESIDUE EDO A 278
08AC8SOFTWAREASN A:104 , GLY A:106 , TYR A:170 , LYS A:174 , HOH A:331BINDING SITE FOR RESIDUE EDO A 279
09AC9SOFTWAREGLY B:64 , GLY B:67 , GLY B:69 , HOH B:308 , HOH B:500 , HOH B:598BINDING SITE FOR RESIDUE K B 272
10BC1SOFTWAREPHE B:108 , TYR B:164 , TRP B:167 , TYR B:170 , HOH B:811BINDING SITE FOR RESIDUE PG5 B 273
11BC2SOFTWAREHOH A:295 , PRO B:81 , TYR B:134 , GLN B:137 , HOH B:682BINDING SITE FOR RESIDUE EDO B 274
12BC3SOFTWAREARG A:54 , ARG B:89 , ALA B:141 , PRO B:142 , HOH B:799BINDING SITE FOR RESIDUE EDO B 275
13BC4SOFTWAREASP B:114BINDING SITE FOR RESIDUE EDO B 276
14BC5SOFTWAREASN B:104 , ALA B:105 , GLY B:106 , TYR B:170 , LYS B:174 , HOH B:365BINDING SITE FOR RESIDUE EDO B 277
15BC6SOFTWARESER B:79 , GLU B:123 , ASP B:126 , HOH B:347BINDING SITE FOR RESIDUE EDO B 278
16BC7SOFTWAREGLY C:64 , GLY C:67 , GLY C:69 , HOH C:356BINDING SITE FOR RESIDUE K C 272
17BC8SOFTWARETYR C:170 , HOH C:814BINDING SITE FOR RESIDUE PG5 C 273
18BC9SOFTWAREARG C:182 , HOH C:730 , ALA D:175 , ARG D:182 , HOH D:643BINDING SITE FOR RESIDUE EDO C 274
19CC1SOFTWAREVAL B:261 , VAL C:261 , PRO C:263 , HOH C:740 , HOH C:742BINDING SITE FOR RESIDUE EDO C 275
20CC2SOFTWAREPRO C:81 , TYR C:134 , GLN C:137 , ALA C:138 , EDO D:274 , HOH D:303BINDING SITE FOR RESIDUE EDO C 276
21CC3SOFTWAREASP C:114 , HOH C:721 , EDO D:275BINDING SITE FOR RESIDUE EDO C 277
22CC4SOFTWAREASN C:104 , ALA C:105 , GLY C:106 , TYR C:170 , LYS C:174BINDING SITE FOR RESIDUE EDO C 278
23CC5SOFTWAREGLY D:64 , GLY D:67 , GLY D:69 , HOH D:308 , HOH D:761BINDING SITE FOR RESIDUE K D 272
24CC6SOFTWAREHOH A:313 , PHE D:108 , TYR D:164 , TRP D:167 , TYR D:170 , HOH D:813BINDING SITE FOR RESIDUE PG5 D 273
25CC7SOFTWAREEDO C:276 , ASP D:114 , MET D:116BINDING SITE FOR RESIDUE EDO D 274
26CC8SOFTWAREEDO C:277 , HOH C:298 , PRO D:81 , TYR D:134 , GLN D:137 , ALA D:138 , HOH D:390BINDING SITE FOR RESIDUE EDO D 275
27CC9SOFTWAREASN D:104 , ALA D:105 , GLY D:106 , THR D:154 , TYR D:170 , LYS D:174 , HOH D:376BINDING SITE FOR RESIDUE EDO D 276

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3RIH)

(-) 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:260
 aligned with B1MJ88_MYCA9 | B1MJ88 from UniProtKB/TrEMBL  Length:271

    Alignment length:260
                                    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
         B1MJ88_MYCA9    12 KVMFDLSARSVLVTGGTKGIGRGIATVFARAGANVAVAARSPRELSSVTAELGELGAGNVIGVRLDVSDPGSCADAARTVVDAFGALDVVCANAGIFPEARLDTMTPEQLSEVLDVNVKGTVYTVQACLAPLTASGRGRVILTSSITGPVTGYPGWSHYGASKAAQLGFMRTAAIELAPRGVTVNAILPGNILTEGLVDMGEEYISGMARSIPMGMLGSPVDIGHLAAFLATDEAGYITGQAIVVDGGQVLPESPDAVNP 271
               SCOP domains d3riha_ A: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee............hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee........hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rih A  12 KVMFDLSARSVLVTGGTKGIGRGIATVFARAGANVAVAARSPRELSSVTAELGELGAGNVIGVRLDVSDPGSCADAARTVVDAFGALDVVCANAGIFPEARLDTMTPEQLSEVLDVNVKGTVYTVQACLAPLTASGRGRVILTSSITGPVTGYPGWSHYGASKAAQLGFMRTAAIELAPRGVTVNAILPGNILTEGLVDMGEEYISGMARSIPMGMLGSPVDIGHLAAFLATDEAGYITGQAIVVDGGQVLPESPDAVNP 271
                                    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


Chain B from PDB  Type:PROTEIN  Length:260
 aligned with B1MJ88_MYCA9 | B1MJ88 from UniProtKB/TrEMBL  Length:271

    Alignment length:260
                                    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
         B1MJ88_MYCA9    12 KVMFDLSARSVLVTGGTKGIGRGIATVFARAGANVAVAARSPRELSSVTAELGELGAGNVIGVRLDVSDPGSCADAARTVVDAFGALDVVCANAGIFPEARLDTMTPEQLSEVLDVNVKGTVYTVQACLAPLTASGRGRVILTSSITGPVTGYPGWSHYGASKAAQLGFMRTAAIELAPRGVTVNAILPGNILTEGLVDMGEEYISGMARSIPMGMLGSPVDIGHLAAFLATDEAGYITGQAIVVDGGQVLPESPDAVNP 271
               SCOP domains d3rihb_ B: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee............hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhh.hhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee........hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rih B  12 KVMFDLSARSVLVTGGTKGIGRGIATVFARAGANVAVAARSPRELSSVTAELGELGAGNVIGVRLDVSDPGSCADAARTVVDAFGALDVVCANAGIFPEARLDTMTPEQLSEVLDVNVKGTVYTVQACLAPLTASGRGRVILTSSITGPVTGYPGWSHYGASKAAQLGFMRTAAIELAPRGVTVNAILPGNILTEGLVDMGEEYISGMARSIPMGMLGSPVDIGHLAAFLATDEAGYITGQAIVVDGGQVLPESPDAVNP 271
                                    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


Chain C from PDB  Type:PROTEIN  Length:259
 aligned with B1MJ88_MYCA9 | B1MJ88 from UniProtKB/TrEMBL  Length:271

    Alignment length:259
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262         
         B1MJ88_MYCA9    13 VMFDLSARSVLVTGGTKGIGRGIATVFARAGANVAVAARSPRELSSVTAELGELGAGNVIGVRLDVSDPGSCADAARTVVDAFGALDVVCANAGIFPEARLDTMTPEQLSEVLDVNVKGTVYTVQACLAPLTASGRGRVILTSSITGPVTGYPGWSHYGASKAAQLGFMRTAAIELAPRGVTVNAILPGNILTEGLVDMGEEYISGMARSIPMGMLGSPVDIGHLAAFLATDEAGYITGQAIVVDGGQVLPESPDAVNP 271
               SCOP domains d3rihc_ 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
                 3rih C  13 VMFDLSARSVLVTGGTKGIGRGIATVFARAGANVAVAARSPRELSSVTAELGELGAGNVIGVRLDVSDPGSCADAARTVVDAFGALDVVCANAGIFPEARLDTMTPEQLSEVLDVNVKGTVYTVQACLAPLTASGRGRVILTSSITGPVTGYPGWSHYGASKAAQLGFMRTAAIELAPRGVTVNAILPGNILTEGLVDMGEEYISGMARSIPMGMLGSPVDIGHLAAFLATDEAGYITGQAIVVDGGQVLPESPDAVNP 271
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262         


Chain D from PDB  Type:PROTEIN  Length:260
 aligned with B1MJ88_MYCA9 | B1MJ88 from UniProtKB/TrEMBL  Length:271

    Alignment length:260
                                    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
         B1MJ88_MYCA9    12 KVMFDLSARSVLVTGGTKGIGRGIATVFARAGANVAVAARSPRELSSVTAELGELGAGNVIGVRLDVSDPGSCADAARTVVDAFGALDVVCANAGIFPEARLDTMTPEQLSEVLDVNVKGTVYTVQACLAPLTASGRGRVILTSSITGPVTGYPGWSHYGASKAAQLGFMRTAAIELAPRGVTVNAILPGNILTEGLVDMGEEYISGMARSIPMGMLGSPVDIGHLAAFLATDEAGYITGQAIVVDGGQVLPESPDAVNP 271
               SCOP domains d3rihd_ D: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------adh_short-3rihD01 D:20-189                                                                                                                                                ---------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------adh_short-3rihD02 D:20-189                                                                                                                                                ---------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) --------adh_short-3rihD03 D:20-189                                                                                                                                                ---------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) --------adh_short-3rihD04 D:20-189                                                                                                                                                ---------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .........eeee....hhhhhhhhhhhhhh..eeeeee....hhhhhhhhhh......eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee............hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhh.hhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee........hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rih D  12 KVMFDLSARSVLVTGGTKGIGRGIATVFARAGANVAVAARSPRELSSVTAELGELGAGNVIGVRLDVSDPGSCADAARTVVDAFGALDVVCANAGIFPEARLDTMTPEQLSEVLDVNVKGTVYTVQACLAPLTASGRGRVILTSSITGPVTGYPGWSHYGASKAAQLGFMRTAAIELAPRGVTVNAILPGNILTEGLVDMGEEYISGMARSIPMGMLGSPVDIGHLAAFLATDEAGYITGQAIVVDGGQVLPESPDAVNP 271
                                    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
   Legend:   → Mismatch (orange background)
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  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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3RIH)

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 Related Entries

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(-) Related Entries Specified in the PDB File

3pk0 SIMILAR PROTEIN FROM MYCOBACTERIUM SMEGMATIS RELATED ID: MYABA.01365.A RELATED DB: TARGETDB