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(-) Description

Title :  THE CRYSTAL STRUCTURE OF OXIDOREDUCTASE (GFO/IDH/MOCA FAMILY) FROM STREPTOCOCCUS PNEUMONIAE TIGR4 IN COMPLEX WITH NADP
 
Authors :  K. Tan, C. Hatzos-Skintges, R. Jedrzejczak, A. Joachimiak, Midwest C Structural Genomics (Mcsg)
Date :  04 Nov 13  (Deposition) - 27 Nov 13  (Release) - 27 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Keywords :  Structural Genomics, Psi-Biology, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, C. Hatzos-Skintges, R. Jedrzejczak, A. Joachimiak
The Crystal Structure Of Oxidoreductase (Gfo/Idh/Moca Family) From Streptococcus Pneumoniae Tigr4 In Complex With Nadp.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - OXIDOREDUCTASE, GFO/IDH/MOCA FAMILY
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SP_1482
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 170187
    Strain: TIGR4

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): AB 
Biological Unit 2 (2x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 20)

Asymmetric Unit (4, 20)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2FMT13Ligand/IonFORMIC ACID
3GOL3Ligand/IonGLYCEROL
4NAP3Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2FMT7Ligand/IonFORMIC ACID
3GOL1Ligand/IonGLYCEROL
4NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 2 (4, 20)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2FMT12Ligand/IonFORMIC ACID
3GOL4Ligand/IonGLYCEROL
4NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:9 , GLY A:10 , ILE A:12 , SER A:33 , ARG A:34 , ALA A:69 , SER A:70 , PRO A:71 , ASN A:72 , LEU A:74 , HIS A:75 , GLU A:92 , LYS A:93 , ARG A:121 , ASN A:164 , PHE A:170 , ASP A:177 , TYR A:181 , FMT A:402 , HOH A:525 , HOH A:527 , HOH A:585 , HOH A:588 , HOH A:589 , HOH A:613 , HOH A:615 , HOH A:625 , HOH A:637 , HOH A:658BINDING SITE FOR RESIDUE NAP A 401
02AC2SOFTWARELYS A:93 , ASP A:177 , LEU A:178 , TYR A:181 , NAP A:401 , HOH A:614BINDING SITE FOR RESIDUE FMT A 402
03AC3SOFTWAREMET A:154 , ASN A:229 , LEU B:141 , HOH B:504BINDING SITE FOR RESIDUE FMT A 403
04AC4SOFTWARETYR A:123 , ARG A:188 , TRP A:299BINDING SITE FOR RESIDUE FMT A 404
05AC5SOFTWARETHR B:9 , GLY B:10 , ILE B:12 , SER B:33 , ARG B:34 , THR B:38 , ALA B:69 , SER B:70 , PRO B:71 , ASN B:72 , LEU B:74 , HIS B:75 , GLU B:92 , LYS B:93 , ARG B:121 , ASN B:164 , PHE B:170 , ASP B:177 , TYR B:181 , FMT B:402 , HOH B:508 , HOH B:517 , HOH B:525 , HOH B:555 , HOH B:558 , HOH B:562 , HOH B:600 , HOH B:611 , HOH B:618 , HOH B:713BINDING SITE FOR RESIDUE NAP B 401
06AC6SOFTWARELYS B:93 , TYR B:181 , NAP B:401 , HOH B:594 , HOH B:653BINDING SITE FOR RESIDUE FMT B 402
07AC7SOFTWAREALA A:143 , GLN A:221 , ASN B:210 , GLY B:211 , ASP B:212 , LYS B:225BINDING SITE FOR RESIDUE FMT B 403
08AC8SOFTWAREHOH B:528BINDING SITE FOR RESIDUE FMT B 404
09AC9SOFTWAREASN B:294 , GLN B:297 , HOH B:623 , VAL C:187 , GLY C:191 , ASP C:302 , ACT C:410 , HOH C:657BINDING SITE FOR RESIDUE FMT B 405
10BC1SOFTWAREGLU B:110 , ASN B:113 , HOH B:674 , LYS C:192 , TYR C:301 , HOH C:601BINDING SITE FOR RESIDUE GOL B 406
11BC2SOFTWARETHR C:9 , GLY C:10 , ILE C:12 , SER C:33 , ARG C:34 , THR C:38 , ALA C:69 , SER C:70 , PRO C:71 , ASN C:72 , LEU C:74 , HIS C:75 , GLU C:92 , LYS C:93 , ARG C:121 , ASN C:164 , PHE C:170 , ASP C:177 , TYR C:181 , FMT C:402 , HOH C:512 , HOH C:529 , HOH C:539 , HOH C:560 , HOH C:588 , HOH C:635 , HOH C:637 , HOH C:668 , HOH C:705BINDING SITE FOR RESIDUE NAP C 401
12BC3SOFTWARELYS C:93 , TYR C:181 , NAP C:401 , HOH C:572BINDING SITE FOR RESIDUE FMT C 402
13BC4SOFTWAREVAL C:96 , SER C:97 , GLN C:98 , PRO C:99 , HIS C:307 , LEU C:310 , HOH C:631BINDING SITE FOR RESIDUE FMT C 403
14BC5SOFTWARETHR C:241 , ASP C:242 , HIS C:261 , HOH C:665 , HOH C:726BINDING SITE FOR RESIDUE FMT C 404
15BC6SOFTWARETRP C:299BINDING SITE FOR RESIDUE FMT C 405
16BC7SOFTWAREPRO C:71 , ASN C:72 , ASN C:164 , VAL C:165 , PHE C:170BINDING SITE FOR RESIDUE FMT C 406
17BC8SOFTWARESER C:151 , LYS C:228BINDING SITE FOR RESIDUE FMT C 407
18BC9SOFTWAREILE B:106 , GLN B:297 , TYR B:301 , ASN C:294 , GLN C:297 , THR C:298 , HOH C:583 , HOH C:609BINDING SITE FOR RESIDUE GOL C 408
19CC1SOFTWAREGLU C:110 , ASN C:113 , PHE C:115 , HOH C:614BINDING SITE FOR RESIDUE GOL C 409
20CC2SOFTWAREGLN B:297 , FMT B:405 , HOH B:623 , LYS C:132 , HOH C:657BINDING SITE FOR RESIDUE ACT C 410

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Lys A:93 -Pro A:94
2Lys B:93 -Pro B:94
3Lys C:93 -Pro C:94

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NHE)

(-) 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:325
                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh.....eee.hhhhhhhh...eeee..hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhh..eeeeeeeee....hhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeeeeee..eeeeeeee........eeeee..eeeee........eeeee....eeee........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nhe A   1 MLKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRKLETAATFASRYQNIQLFDQLEVFFKSSFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIKNFLADKQVLGADFNYAKYSSKMPDLLAGQTPNVFSDRFAGGALMDLGIYPLYAAVRLFGKANDATYHAQQLDNSIDLNGDGILFYPDYQVHIKAGKNITSNLPCEIYTTDGTLTLNTIEHIRSAIFTDHQGNQVQLPIQQAPHTMTEEVAAFAHMIQQPDLNLYQTWLYDAGSVHELLYTMRQTAGIRFEAEK 325
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320     


Chain B from PDB  Type:PROTEIN  Length:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh.....eee.hhhhhhhh...eeee..hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh...eeeeeeeee....hhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeeeee....eeeeeee........eeeee..eeeee........eeeee....eee.........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nhe B   0 AMLKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRKLETAATFASRYQNIQLFDQLEVFFKSSFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIKNFLADKQVLGADFNYAKYSSKMPDLLAGQTPNVFSDRFAGGALMDLGIYPLYAAVRLFGKANDATYHAQQLDNSIDLNGDGILFYPDYQVHIKAGKNITSNLPCEIYTTDGTLTLNTIEHIRSAIFTDHQGNQVQLPIQQAPHTMTEEVAAFAHMIQQPDLNLYQTWLYDAGSVHELLYTMRQTAGIRFEAEK 325
                                     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       259       269       279       289       299       309       319      


Chain C from PDB  Type:PROTEIN  Length:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh.....eee.hhhhhh.....eeee..hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh...eeeeeeeee....hhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeeeee....eeeeeee........eeeee..eeeee........eeeee....eee.........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nhe C   0 AMLKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRKLETAATFASRYQNIQLFDQLEVFFKSSFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIKNFLADKQVLGADFNYAKYSSKMPDLLAGQTPNVFSDRFAGGALMDLGIYPLYAAVRLFGKANDATYHAQQLDNSIDLNGDGILFYPDYQVHIKAGKNITSNLPCEIYTTDGTLTLNTIEHIRSAIFTDHQGNQVQLPIQQAPHTMTEEVAAFAHMIQQPDLNLYQTWLYDAGSVHELLYTMRQTAGIRFEAEK 325
                                     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       259       269       279       289       299       309       319
   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

(no "SCOP Domain" information available for 4NHE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4NHE)

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  A0A0H2UR04_S | A0A0H2UR04
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 Related Entries

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        A0A0H2UR04_S | A0A0H2UR04: 2ho5 4iq0

(-) Related Entries Specified in the PDB File

2ho5 SEMET LABLED RELATED ID: MCSG-APC111382 RELATED DB: TARGETTRACK
4iq0 SEMET LABLED AND LYSINE METHYLATED