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(-) Description

Title :  CRYSTAL STRUCTURE OF L-LACTATE DEHYDROGENASE FROM BACILLUS CEREUS ATCC 14579 COMPLEXED WITH CALCIUM, NYSGRC TARGET 029452
 
Authors :  V. N. Malashkevich, J. B. Bonanno, R. Bhosle, R. Toro, B. Hillerich, A. G S. Garforth, A. Kar, M. K. Chan, J. Lafluer, H. Patel, B. Matikainen, S. S. Lim, A. Celikgil, G. Villegas, B. Evans, J. Love, A. Fiser, K. Khafiz R. Seidel, S. C. Almo, New York Structural Genomics Research Con (Nysgrc)
Date :  11 Jul 13  (Deposition) - 24 Jul 13  (Release) - 24 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Protein Structure Initiative, Nysgrc, Psi- Biology, New York Structural Genomics Research Consortium, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. N. Malashkevich, J. B. Bonanno, R. Bhosle, R. Toro, B. Hillerich, A. Gizzi, S. Garforth, A. Kar, M. K. Chan, J. Lafluer, H. Patel, B. Matikainen, S. Chamala, S. Lim, A. Celikgil, G. Villegas, B. Evans, J. Love, A. Fiser, K. Khafizov, R. Seidel, S. C. Almo
Crystal Structure Of L-Lactate Dehydrogenase From Bacillus Cereus Atcc 14579 Complexed With Calcium, Nysgrc Target 029452
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - L-LACTATE DEHYDROGENASE 1
    Chains: A, B, C, D
    EC Number: 1.1.1.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)CODON+RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BC_1924, LDH, LDH1
    Organism Scientific: BACILLUS CEREUS
    Organism Taxid: 226900
    Strain: ATCC 14579
    Synonym: L-LDH 1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 34)

Asymmetric/Biological Unit (2, 34)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
2MSE28Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:624 , HOH A:650 , HOH A:684 , HOH A:686 , HOH C:622 , HOH C:632 , HOH C:648 , HOH C:649BINDING SITE FOR RESIDUE CA A 500
2AC2SOFTWARELYS A:3 , ILE A:5 , ASP A:75 , HOH A:654 , HOH A:672 , HOH A:688 , HOH A:689BINDING SITE FOR RESIDUE CA A 501
3AC3SOFTWAREHOH B:627 , HOH B:643 , HOH D:627 , HOH D:642 , HOH D:662BINDING SITE FOR RESIDUE CA B 500
4AC4SOFTWARELYS B:3 , ILE B:5 , ASP B:75 , HOH B:650 , HOH B:657BINDING SITE FOR RESIDUE CA B 501
5AC5SOFTWARELYS C:3 , ILE C:5 , ASP C:75 , HOH C:650 , HOH C:655 , HOH C:664 , HOH C:672BINDING SITE FOR RESIDUE CA C 501
6AC6SOFTWARELYS D:3 , ILE D:5 , ASP D:75 , HOH D:643 , HOH D:653 , HOH D:670 , HOH D:674BINDING SITE FOR RESIDUE CA D 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LN1)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asn A:123 -Pro A:124
2Asn B:123 -Pro B:124
3Asn C:123 -Pro C:124
4Asn D:123 -Pro D:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LN1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LN1)

(-) Exons   (0, 0)

(no "Exon" information available for 4LN1)

(-) 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:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4ln1a1 A:-6-147 automated matches                                                                                                                    d4ln1a2 A:148-314 automated matches                                                                                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee.......hhhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ln1 A  -6 ENLYFQSmKKGINRVVLVGTGAVGCSYAYCmINQAVAEEFVLVDVNEAKAEGEAmDLSHAVPFAPAPTRVWKGSYEDCKDADLVVITAGLPQTRLDLVEKNAKIFKQIVRSImDSGFDGIFLIATNPVDILTYVTWKESGLPKERVIGSGTTLDSARFRYmLGEYFDIGPHNIHAYIIGEHGDTELPVWSHVSVGIQKLQTLLEKDNTYNQEDLDKIFINVRDAAYHIIERKGATYYGIGmSLLRVTKAILNDENSVLTVSAYLEGQYGQKDVYIGVPAVLNRGGVREILEVELSEDEELKFDHSVQVLKETmAPVL 314
                                   | 3        13        23|       33        43    |   53        63        73        83 ||     97       107  |    117       127       137       147       157|      167       177       187       197       207       217       227       237|      247       257       267       277       287       297       307  |    
                                   1-MSE                 24-MSE                  48-MSE                               85|                 110-MSE                                         158-MSE                                                                         238-MSE                                                                 310-MSE
                                                                                                                       90                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:321
                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4ln1b1 B:-6-147 automated matches                                                                                                                        d4ln1b2 B:148-314 automated matches                                                                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ln1 B  -6 ENLYFQSmKKGINRVVLVGTGAVGCSYAYCmINQAVAEEFVLVDVNEAKAEGEAmDLSHAVPFAPAPTRVWKGSYEDCKDADLVVITAGLPQKPGETRLDLVEKNAKIFKQIVRSImDSGFDGIFLIATNPVDILTYVTWKESGLPKERVIGSGTTLDSARFRYmLGEYFDIGPHNIHAYIIGEHGDTELPVWSHVSVGIQKLQTLLEKDNTYNQEDLDKIFINVRDAAYHIIERKGATYYGIGmSLLRVTKAILNDENSVLTVSAYLEGQYGQKDVYIGVPAVLNRGGVREILEVELSEDEELKFDHSVQVLKETmAPVL 314
                                   | 3        13        23|       33        43    |   53        63        73        83        93       103      |113       123       133       143       153    |  163       173       183       193       203       213       223       233    |  243       253       263       273       283       293       303      |313 
                                   1-MSE                 24-MSE                  48-MSE                                                       110-MSE                                         158-MSE                                                                         238-MSE                                                                 310-MSE


Chain C from PDB  Type:PROTEIN  Length:316
                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4ln1c1 C:-6-147 automated matches                                                                                                                   d4ln1c2 C:148-314 automated matches                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee......hhhhhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhh..hhh.ee..ee.......ee.hhh.ee..eehhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eee..eeeee.hhh.eeeeee..eeee..eeeee.....hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ln1 C  -6 ENLYFQSmKKGINRVVLVGTGAVGCSYAYCmINQAVAEEFVLVDVNEAKAEGEAmDLSHAVPFAPAPTRVWKGSYEDCKDADLVVITAGLPTRLDLVEKNAKIFKQIVRSImDSGFDGIFLIATNPVDILTYVTWKESGLPKERVIGSGTTLDSARFRYmLGEYFDIGPHNIHAYIIGEHGDTELPVWSHVSVGIQKLQTLLEKDNTYNQEDLDKIFINVRDAAYHIIERKGATYYGIGmSLLRVTKAILNDENSVLTVSAYLEGQYGQKDVYIGVPAVLNRGGVREILEVELSEDEELKFDHSVQVLKETmAPVL 314
                                   | 3        13        23|       33        43    |   53        63        73        83||      98       108 |     118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308 |    
                                   1-MSE                 24-MSE                  48-MSE                              84|                 110-MSE                                         158-MSE                                                                         238-MSE                                                                 310-MSE
                                                                                                                      90                                                                                                                                                                                                                                


Chain D from PDB  Type:PROTEIN  Length:315
                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4ln1d1 D:-6-147 automated matches                                                                                                                  d4ln1d2 D:148-314 automated matches                                                                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee......hhhhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eee..eeeee.hhh.eeeeee..eeee..eeeee.....hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ln1 D  -6 ENLYFQSmKKGINRVVLVGTGAVGCSYAYCmINQAVAEEFVLVDVNEAKAEGEAmDLSHAVPFAPAPTRVWKGSYEDCKDADLVVITAGLPRLDLVEKNAKIFKQIVRSImDSGFDGIFLIATNPVDILTYVTWKESGLPKERVIGSGTTLDSARFRYmLGEYFDIGPHNIHAYIIGEHGDTELPVWSHVSVGIQKLQTLLEKDNTYNQEDLDKIFINVRDAAYHIIERKGATYYGIGmSLLRVTKAILNDENSVLTVSAYLEGQYGQKDVYIGVPAVLNRGGVREILEVELSEDEELKFDHSVQVLKETmAPVL 314
                                   | 3        13        23|       33        43    |   53        63        73        83||      99       109|      119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309|    
                                   1-MSE                 24-MSE                  48-MSE                              84|                110-MSE                                         158-MSE                                                                         238-MSE                                                                 310-MSE
                                                                                                                      91
   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  (2, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LN1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LN1)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        LDH1_BACCR | Q81EP4: 4lmr

(-) Related Entries Specified in the PDB File

4lmr RELATED ID: NYSGRC-029452 RELATED DB: TARGETTRACK