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(-) Description

Title :  CRYSTAL STRUCTURE OF A SHORT CHAIN ALCOHOL DEHYDROGENASE-RELATED DEHYDROGENASE (TARGET ID NYSGRC-011812) FROM SINORHIZOBIUM MELILOTI 1021 IN SPACE GROUP P21
 
Authors :  A. Ghosh, S. C. Almo, New York Structural Genomics Research Conso (Nysgrc)
Date :  10 Sep 12  (Deposition) - 19 Sep 12  (Release) - 19 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Psi-Biology, Nysgrc, New York Structural Genomics Research Consortium, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Ghosh, R. Bhoshle, R. Toro, A. Gizzi, B. Hillerich, R. Seidel, S. C. Almo, New York Structural Genomics Research Consortium
Crystal Structure Of A Short Chain Alcohol Dehydrogenase-Related Dehydrogenase (Target Id Nysgrc-011812) From Sinorhizobium Meliloti 1021 In Space Group P21
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SHORT CHAIN ALCOHOL DEHYDROGENASE-RELATED DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSGC-HIS
    Expression System Strain: BL21 (DE3) PRIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RA0888, SMA1629
    Organism Scientific: SINORHIZOBIUM MELILOTI
    Organism Taxid: 266834
    Strain: 1021

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 87)

Asymmetric/Biological Unit (4, 87)
No.NameCountTypeFull Name
1CA11Ligand/IonCALCIUM ION
2CL40Ligand/IonCHLORIDE ION
3MPD12Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4MSE24Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (63, 63)

Asymmetric Unit (63, 63)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:96 , ASP A:101 , HOH A:407 , HOH A:412 , HOH A:415BINDING SITE FOR RESIDUE CA A 301
02AC2SOFTWARELYS A:163 , SER A:166 , LYS A:167 , PRO D:219 , GLY D:254BINDING SITE FOR RESIDUE CL A 302
03AC3SOFTWAREGLY A:20 , GLU A:187 , CL A:306 , HOH A:514BINDING SITE FOR RESIDUE CL A 303
04AC4SOFTWARELEU A:144 , PRO A:145 , GLU A:146BINDING SITE FOR RESIDUE CL A 304
05AC5SOFTWARELEU A:5 , ASN A:6BINDING SITE FOR RESIDUE CL A 305
06AC6SOFTWARELYS A:19 , THR A:186 , GLU A:187 , ALA A:188 , CL A:303 , HOH A:559 , HOH A:570BINDING SITE FOR RESIDUE CL A 306
07AC7SOFTWAREMSE A:212 , GLY A:217 , ILE A:218 , HOH A:478 , HOH A:524BINDING SITE FOR RESIDUE CL A 307
08AC8SOFTWAREARG A:118 , GLN A:119BINDING SITE FOR RESIDUE CL A 308
09AC9SOFTWARELYS A:167 , HOH A:530 , HOH D:611 , HOH D:690BINDING SITE FOR RESIDUE CL A 309
10BC1SOFTWAREVAL A:141 , ALA B:259 , CL B:307 , HOH B:545BINDING SITE FOR RESIDUE CL A 310
11BC2SOFTWAREASP A:99 , HOH A:425 , HOH C:515BINDING SITE FOR RESIDUE CL A 311
12BC3SOFTWAREGLY A:130 , GLY A:173 , HOH A:488 , HOH A:561 , HOH A:623BINDING SITE FOR RESIDUE CL A 312
13BC4SOFTWAREARG A:115 , ARG A:118 , HOH A:448BINDING SITE FOR RESIDUE CL A 313
14BC5SOFTWAREPHE A:4 , LEU A:5 , SER C:-1 , PHE D:4 , LEU D:5BINDING SITE FOR RESIDUE CL A 314
15BC6SOFTWARETHR A:15 , HIS A:82 , HOH A:413BINDING SITE FOR RESIDUE CL A 315
16BC7SOFTWAREGLN A:139 , TRP A:183 , MPD A:318 , HOH A:581 , HOH A:597BINDING SITE FOR RESIDUE MPD A 316
17BC8SOFTWAREMSE A:83 , LEU A:84 , GLY A:85 , GLY A:86 , VAL A:135 , TYR A:151 , LYS A:155 , ILE A:184BINDING SITE FOR RESIDUE MPD A 317
18BC9SOFTWAREGLY A:86 , SER A:87 , SER A:189 , MPD A:316BINDING SITE FOR RESIDUE MPD A 318
19CC1SOFTWAREALA B:96 , ASP B:101 , CA B:303 , HOH B:409 , HOH B:421 , HOH B:456 , HOH B:509 , HOH B:615BINDING SITE FOR RESIDUE CA B 301
20CC2SOFTWARELYS B:163 , GLY B:246 , VAL C:256 , THR C:258 , HOH C:417 , HOH C:420 , HOH C:470BINDING SITE FOR RESIDUE CA B 302
21CC3SOFTWARESER B:98 , ASP B:101 , CA B:301 , HOH B:434 , HOH B:509 , HOH B:529 , HOH B:615BINDING SITE FOR RESIDUE CA B 303
22CC4SOFTWARELYS B:163 , SER B:166 , LYS B:167 , PRO C:219 , GLY C:254BINDING SITE FOR RESIDUE CL B 304
23CC5SOFTWARETHR B:15 , HIS B:82 , HOH B:402BINDING SITE FOR RESIDUE CL B 305
24CC6SOFTWAREGLY B:20 , GLU B:187 , HOH B:566BINDING SITE FOR RESIDUE CL B 306
25CC7SOFTWARECL A:310 , HOH A:435 , ALA B:259 , ARG C:140BINDING SITE FOR RESIDUE CL B 307
26CC8SOFTWAREARG B:43 , VAL B:53 , GLU B:54 , HOH B:589BINDING SITE FOR RESIDUE CL B 308
27CC9SOFTWAREARG B:115 , ARG B:118 , HOH B:579BINDING SITE FOR RESIDUE CL B 309
28DC1SOFTWAREGLU B:205BINDING SITE FOR RESIDUE CL B 310
29DC2SOFTWAREILE B:2 , PHE B:4 , LEU B:5 , PHE C:4 , LEU C:5 , SER D:-1BINDING SITE FOR RESIDUE CL B 311
30DC3SOFTWARELEU B:144 , PRO B:145 , GLU B:146 , HOH B:560BINDING SITE FOR RESIDUE CL B 312
31DC4SOFTWAREGLN B:139 , TRP B:183 , MPD B:314 , HOH B:552 , HOH B:616BINDING SITE FOR RESIDUE MPD B 313
32DC5SOFTWAREGLY B:86 , SER B:87 , MPD B:313 , HOH B:555BINDING SITE FOR RESIDUE MPD B 314
33DC6SOFTWAREMSE B:83 , GLY B:85 , GLY B:86 , THR B:136 , TYR B:151 , LYS B:155 , ILE B:184 , HOH B:465BINDING SITE FOR RESIDUE MPD B 315
34DC7SOFTWAREALA C:96 , ASP C:101 , HOH C:437 , HOH C:441 , HOH C:449 , HOH C:522 , HOH C:572BINDING SITE FOR RESIDUE CA C 301
35DC8SOFTWAREGLY C:216 , GLY C:217 , THR C:255 , HOH C:433 , HOH C:444 , HOH C:531 , HOH C:557BINDING SITE FOR RESIDUE CA C 302
36DC9SOFTWAREILE C:184 , THR C:186 , SER C:189 , CL C:310 , MPD C:315 , HOH C:570 , HOH C:590BINDING SITE FOR RESIDUE CA C 303
37EC1SOFTWARELYS C:163 , SER C:166 , LYS C:167BINDING SITE FOR RESIDUE CL C 304
38EC2SOFTWARETHR C:186 , GLU C:187 , ALA C:188 , CL C:309 , HOH C:578 , HOH C:579BINDING SITE FOR RESIDUE CL C 305
39EC3SOFTWAREHOH B:436 , HOH B:536 , LYS C:167 , HOH C:508 , HOH C:656BINDING SITE FOR RESIDUE CL C 306
40EC4SOFTWAREARG B:140 , ALA C:259 , HOH C:646 , VAL D:141 , HOH D:541BINDING SITE FOR RESIDUE CL C 307
41EC5SOFTWAREGLU A:185 , HOH A:549 , ASP C:203 , LEU C:204BINDING SITE FOR RESIDUE CL C 308
42EC6SOFTWAREGLY C:20 , GLU C:187 , CL C:305BINDING SITE FOR RESIDUE CL C 309
43EC7SOFTWAREILE C:184 , CA C:303 , MPD C:315 , HOH C:564BINDING SITE FOR RESIDUE CL C 310
44EC8SOFTWARETHR C:15 , HIS C:82 , HOH C:411BINDING SITE FOR RESIDUE CL C 311
45EC9SOFTWAREHOH A:603 , LEU C:144 , PRO C:145 , GLU C:146BINDING SITE FOR RESIDUE CL C 312
46FC1SOFTWAREGLN C:139 , LEU C:144 , MPD C:315 , HOH C:563 , HOH C:628BINDING SITE FOR RESIDUE MPD C 313
47FC2SOFTWAREASP A:99 , TYR A:103 , PHE C:111 , ARG C:115BINDING SITE FOR RESIDUE MPD C 314
48FC3SOFTWAREGLY C:86 , SER C:87 , SER C:189 , CA C:303 , CL C:310 , MPD C:313 , HOH C:649BINDING SITE FOR RESIDUE MPD C 315
49FC4SOFTWAREGLY C:85 , GLY C:86 , THR C:136 , TYR C:151 , LYS C:155 , HOH C:565 , HOH C:573 , HOH C:585 , HOH C:657BINDING SITE FOR RESIDUE MPD C 316
50FC5SOFTWAREALA D:96 , ASP D:101 , HOH D:526 , HOH D:532 , HOH D:586 , HOH D:726 , HOH D:735BINDING SITE FOR RESIDUE CA D 301
51FC6SOFTWAREHOH B:439 , HOH B:613 , HOH D:542 , HOH D:550 , HOH D:577 , HOH D:648BINDING SITE FOR RESIDUE CA D 302
52FC7SOFTWAREGLY D:216 , HOH D:528 , HOH D:548 , HOH D:597 , HOH D:719BINDING SITE FOR RESIDUE CA D 303
53FC8SOFTWAREGLY D:173 , HOH D:561 , HOH D:600 , HOH D:628 , HOH D:686BINDING SITE FOR RESIDUE CA D 304
54FC9SOFTWARELYS D:163 , SER D:166 , LYS D:167BINDING SITE FOR RESIDUE CL D 305
55GC1SOFTWARETHR D:186 , GLU D:187 , ALA D:188 , CL D:310BINDING SITE FOR RESIDUE CL D 306
56GC2SOFTWARETHR D:15 , HIS D:82 , HOH D:658BINDING SITE FOR RESIDUE CL D 307
57GC3SOFTWAREILE D:184BINDING SITE FOR RESIDUE CL D 308
58GC4SOFTWAREGLY D:76 , VAL D:77 , ARG D:127 , HOH D:547 , HOH D:668BINDING SITE FOR RESIDUE CL D 309
59GC5SOFTWAREGLY D:20 , GLU D:187 , CL D:306BINDING SITE FOR RESIDUE CL D 310
60GC6SOFTWAREGLN D:72 , ARG D:73BINDING SITE FOR RESIDUE CL D 311
61GC7SOFTWAREARG D:115 , ARG D:118 , HOH D:501 , HOH D:537 , HOH D:704BINDING SITE FOR RESIDUE CL D 312
62GC8SOFTWAREGLN D:139 , MPD D:314 , HOH D:656 , HOH D:731BINDING SITE FOR RESIDUE MPD D 313
63GC9SOFTWAREGLY D:86 , SER D:87 , SER D:189 , MPD D:313 , HOH D:676BINDING SITE FOR RESIDUE MPD D 314

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H15)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4H15)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H15)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H15)

(-) Exons   (0, 0)

(no "Exon" information available for 4H15)

(-) 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:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains d4h15a_ A: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeee....hhhhhhhhhhhhhh..eeeeee...........eee....hhhhhhhhhhhhhhhh....eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhh..hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h15 A  -1 SmmIEFLNLRGKRALITAGTKGAGAATVSLFLELGAQVLTTARARPEGLPEELFVEADLTTKEGCAIVAEATRQRLGGVDVIVHmLGGSSAAGGGFSALSDDDWYNELSLNLFAAVRLDRQLVPDmVARGSGVVVHVTSIQRVLPLPESTTAYAAAKAALSTYSKAmSKEVSPKGVRVVRVSPGWIETEASVRLAERLAKQAGTDLEGGKKIImDGLGGIPLGRPAKPEEVANLIAFLASDRAASITGAEYTIDGGTVPTA 259
                             ||      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 
                             ||                                                                                83-MSE                                  124-MSE                                  165-MSE                                        212-MSE                                           
                             0-MSE                                                                                                                                                                                                                                                               
                              1-MSE                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains d4h15b_ B: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeee....hhhhhhhhhhhhhh..eeeeee...........eee....hhhhhhhhhhhhhhhh....eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h15 B  -1 SmmIEFLNLRGKRALITAGTKGAGAATVSLFLELGAQVLTTARARPEGLPEELFVEADLTTKEGCAIVAEATRQRLGGVDVIVHmLGGSSAAGGGFSALSDDDWYNELSLNLFAAVRLDRQLVPDmVARGSGVVVHVTSIQRVLPLPESTTAYAAAKAALSTYSKAmSKEVSPKGVRVVRVSPGWIETEASVRLAERLAKQAGTDLEGGKKIImDGLGGIPLGRPAKPEEVANLIAFLASDRAASITGAEYTIDGGTVPTA 259
                             ||      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 
                             0-MSE                                                                             83-MSE                                  124-MSE                                  165-MSE                                        212-MSE                                           
                              1-MSE                                                                                                                                                                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains d4h15c_ C: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeee....hhhhhhhhhhhhhh..eeeeee.......hhh.eee....hhhhhhhhhhhhhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h15 C  -1 SmmIEFLNLRGKRALITAGTKGAGAATVSLFLELGAQVLTTARARPEGLPEELFVEADLTTKEGCAIVAEATRQRLGGVDVIVHmLGGSSAAGGGFSALSDDDWYNELSLNLFAAVRLDRQLVPDmVARGSGVVVHVTSIQRVLPLPESTTAYAAAKAALSTYSKAmSKEVSPKGVRVVRVSPGWIETEASVRLAERLAKQAGTDLEGGKKIImDGLGGIPLGRPAKPEEVANLIAFLASDRAASITGAEYTIDGGTVPTA 259
                             ||      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 
                             0-MSE                                                                             83-MSE                                  124-MSE                                  165-MSE                                        212-MSE                                           
                              1-MSE                                                                                                                                                                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains d4h15d_ D: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeee....hhhhhhhhhhhhhh..eeeeee.......hhh.eee....hhhhhhhhhhhhhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h15 D  -1 SmmIEFLNLRGKRALITAGTKGAGAATVSLFLELGAQVLTTARARPEGLPEELFVEADLTTKEGCAIVAEATRQRLGGVDVIVHmLGGSSAAGGGFSALSDDDWYNELSLNLFAAVRLDRQLVPDmVARGSGVVVHVTSIQRVLPLPESTTAYAAAKAALSTYSKAmSKEVSPKGVRVVRVSPGWIETEASVRLAERLAKQAGTDLEGGKKIImDGLGGIPLGRPAKPEEVANLIAFLASDRAASITGAEYTIDGGTVPTA 259
                             ||      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 
                             0-MSE                                                                             83-MSE                                  124-MSE                                  165-MSE                                        212-MSE                                           
                              1-MSE
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H15)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H15)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4h15)
 

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  4h15
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  Q92YJ2_RHIME | Q92YJ2
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  1.1.1.-
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 Related Entries

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

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        Q92YJ2_RHIME | Q92YJ2: 4h16

(-) Related Entries Specified in the PDB File

4h16