Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF GAMMA-HYDROXYBUTYRATE DEHYDROGENASE FROM GEOBACTER SULFURREDUCENS IN COMPLEX WITH NADP+
 
Authors :  Y. Zhang, R. M. Garavito
Date :  25 Oct 10  (Deposition) - 11 Jan 12  (Release) - 01 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E (2x),G (2x)
Biol. Unit 3:  F (1x),H (1x)
Keywords :  Gamma-Hydroxybutyrate Dehydrogenase, Succinic Semialdehyde Reductase, Glyoxylate Metabolism, Geobacter Sulfurreducens, Dehydrogenase/Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zhang, Y. Zheng, L. Qin, S. Wang, G. W. Buchko, R. M. Garavito
Structural Characterization Of A Beta-Hydroxyacid Dehydrogenase From Geobacter Sulfurreducens And Geobacter Metallireducens With Succinic Semialdehyde Reductase Activity.
Biochimie V. 104 61 2014
PubMed-ID: 24878278  |  Reference-DOI: 10.1016/J.BIOCHI.2014.05.002

(-) Compounds

Molecule 1 - 3-HYDROXYISOBUTYRATE DEHYDROGENASE FAMILY PROTEIN
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PLW01
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GSU1372
    Organism Scientific: GEOBACTER SULFURREDUCENS
    Organism Taxid: 35554

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABCD    
Biological Unit 2 (2x):     E (2x) G (2x) 
Biological Unit 3 (1x):      F (1x) H (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 19)

Asymmetric Unit (2, 19)
No.NameCountTypeFull Name
1GOL11Ligand/IonGLYCEROL
2NAP8Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:8 , LEU A:9 , GLY A:10 , ILE A:11 , MET A:12 , ASN A:31 , ARG A:32 , ASN A:33 , MET A:64 , LEU A:65 , ALA A:66 , ALA A:70 , GLU A:73 , VAL A:74 , THR A:96 , VAL A:121 , GLY A:123 , THR A:124 , LYS A:125 , LYS A:171 , SER A:231 , PHE A:232 , PRO A:233 , HIS A:236 , LYS A:239 , HOH A:308 , HOH A:310 , HOH A:325 , HOH A:362 , HOH A:437 , HOH A:560 , HOH A:630 , HOH A:740 , HOH A:1011 , HOH A:1186 , HOH A:1423BINDING SITE FOR RESIDUE NAP A 301
02AC2SOFTWAREARG A:250 , HOH A:410 , ARG B:242 , GLU B:246BINDING SITE FOR RESIDUE GOL A 304
03AC3SOFTWAREARG A:242 , GLU A:246 , HOH A:754 , ARG B:250 , HOH B:1791 , HOH B:1797BINDING SITE FOR RESIDUE GOL B 304
04AC4SOFTWAREGLY B:8 , LEU B:9 , GLY B:10 , ILE B:11 , MET B:12 , ASN B:31 , ARG B:32 , ASN B:33 , MET B:64 , LEU B:65 , ALA B:66 , ALA B:70 , GLU B:73 , VAL B:74 , THR B:96 , VAL B:121 , GLY B:123 , THR B:124 , SER B:231 , PHE B:232 , HIS B:236 , LYS B:239 , HOH B:292 , HOH B:296 , HOH B:317 , HOH B:555 , HOH B:564 , HOH B:603 , HOH B:918 , HOH B:925 , HOH B:1116 , HOH B:1534 , HOH B:1589BINDING SITE FOR RESIDUE NAP B 301
05AC5SOFTWAREGLY B:131 , GLY B:155 , LYS B:156 , HOH B:303 , HOH B:312 , HOH B:539 , HOH B:541 , HOH B:760BINDING SITE FOR RESIDUE GOL B 305
06AC6SOFTWAREGLY C:8 , LEU C:9 , GLY C:10 , ILE C:11 , MET C:12 , ASN C:31 , ARG C:32 , ASN C:33 , MET C:64 , LEU C:65 , ALA C:66 , ALA C:70 , GLU C:73 , VAL C:74 , THR C:96 , VAL C:121 , GLY C:123 , THR C:124 , LYS C:171 , SER C:231 , PHE C:232 , HIS C:236 , LYS C:239 , HOH C:297 , HOH C:314 , HOH C:818 , HOH C:971 , HOH C:1099 , HOH C:1102 , HOH C:1510 , HOH C:1557 , HOH C:1567BINDING SITE FOR RESIDUE NAP C 301
07AC7SOFTWAREARG C:242 , GLU C:246 , HOH C:474 , ARG D:250BINDING SITE FOR RESIDUE GOL C 304
08AC8SOFTWAREARG C:250 , HOH C:581 , ARG D:242 , GLU D:246BINDING SITE FOR RESIDUE GOL C 288
09AC9SOFTWAREGLY D:8 , LEU D:9 , GLY D:10 , ILE D:11 , MET D:12 , ASN D:31 , ARG D:32 , ASN D:33 , LYS D:36 , MET D:64 , LEU D:65 , ALA D:66 , ALA D:70 , GLU D:73 , VAL D:74 , THR D:96 , VAL D:121 , GLY D:123 , THR D:124 , LYS D:171 , SER D:231 , PHE D:232 , PRO D:233 , HIS D:236 , LYS D:239 , HOH D:296 , HOH D:312 , HOH D:316 , HOH D:339 , HOH D:554 , HOH D:800 , HOH D:938 , HOH D:1097 , HOH D:1439BINDING SITE FOR RESIDUE NAP D 301
10BC1SOFTWAREGLU D:227 , PHE D:228 , PRO D:229 , GLU D:276 , HOH D:656 , ALA F:52 , ASN F:79BINDING SITE FOR RESIDUE GOL D 305
11BC2SOFTWAREGLY E:8 , LEU E:9 , GLY E:10 , ILE E:11 , MET E:12 , ASN E:31 , ARG E:32 , ASN E:33 , MET E:64 , LEU E:65 , ALA E:66 , ALA E:70 , GLU E:73 , VAL E:74 , THR E:96 , VAL E:121 , GLY E:123 , THR E:124 , SER E:231 , PHE E:232 , PRO E:233 , HIS E:236 , LYS E:239 , HOH E:317 , HOH E:451 , HOH E:913 , HOH E:1016 , HOH E:1081 , HOH E:1109 , HOH E:1132 , HOH E:1284 , HOH E:1498 , HOH E:1598BINDING SITE FOR RESIDUE NAP E 301
12BC3SOFTWAREARG E:242 , GLU E:246 , HOH E:1345 , GLU G:246 , ARG G:250 , HOH G:717BINDING SITE FOR RESIDUE GOL E 304
13BC4SOFTWAREGLY F:8 , LEU F:9 , GLY F:10 , ILE F:11 , MET F:12 , ASN F:31 , ARG F:32 , ASN F:33 , MET F:64 , LEU F:65 , ALA F:66 , ALA F:70 , GLU F:73 , VAL F:74 , THR F:96 , VAL F:121 , GLY F:123 , THR F:124 , SER F:231 , PHE F:232 , PRO F:233 , HIS F:236 , LYS F:239 , HOH F:292 , HOH F:293 , HOH F:339 , HOH F:348 , HOH F:350 , HOH F:456 , HOH F:466 , HOH F:478 , HOH F:617 , HOH F:779 , HOH F:1009 , HOH F:1021BINDING SITE FOR RESIDUE NAP F 301
14BC5SOFTWAREARG F:242 , GLU F:246 , HOH F:766 , ARG H:250BINDING SITE FOR RESIDUE GOL F 304
15BC6SOFTWAREGLU F:246 , ARG F:250 , HOH F:1104 , ARG H:242 , GLU H:246 , HOH H:330BINDING SITE FOR RESIDUE GOL F 288
16BC7SOFTWAREGLY G:8 , LEU G:9 , GLY G:10 , ILE G:11 , MET G:12 , ASN G:31 , ARG G:32 , ASN G:33 , MET G:64 , LEU G:65 , ALA G:66 , ALA G:70 , GLU G:73 , VAL G:74 , THR G:96 , VAL G:121 , GLY G:123 , THR G:124 , LYS G:171 , SER G:231 , PHE G:232 , PRO G:233 , HIS G:236 , LYS G:239 , HOH G:294 , HOH G:593 , HOH G:857 , HOH G:1495BINDING SITE FOR RESIDUE NAP G 301
17BC8SOFTWAREARG E:250 , HOH E:1178 , ARG G:242 , GLU G:246BINDING SITE FOR RESIDUE GOL G 304
18BC9SOFTWAREHOH B:541 , HOH B:773 , ASN H:19 , ASP H:130 , ALA H:152 , ALA H:153 , HOH H:477 , HOH H:540 , HOH H:1018BINDING SITE FOR RESIDUE GOL H 305
19CC1SOFTWAREGLY H:8 , LEU H:9 , GLY H:10 , ILE H:11 , MET H:12 , ASN H:31 , ARG H:32 , ASN H:33 , MET H:64 , LEU H:65 , ALA H:66 , ALA H:70 , GLU H:73 , VAL H:74 , THR H:96 , VAL H:121 , GLY H:123 , THR H:124 , SER H:231 , PHE H:232 , PRO H:233 , HIS H:236 , LYS H:239 , HOH H:314 , HOH H:319 , HOH H:321 , HOH H:322 , HOH H:325 , HOH H:331 , HOH H:395 , HOH H:484 , HOH H:759 , HOH H:876 , HOH H:1064 , HOH H:1206BINDING SITE FOR RESIDUE NAP H 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3PDU)

(-) 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:287
 aligned with Q74DE4_GEOSL | Q74DE4 from UniProtKB/TrEMBL  Length:286

    Alignment length:287
                                                                                                                                                                                                                                                                                                                       286 
                                    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     | 
         Q74DE4_GEOSL     1 MTTYGFLGLGIMGGPMAANLVRAGFDVTVWNRNPAKCAPLVALGARQASSPAEVCAACDITIAMLADPAAAREVCFGANGVLEGIGGGRGYIDMSTVDDETSTAIGAAVTARGGRFLEAPVSGTKKPAEDGTLIILAAGDQSLFTDAGPAFAALGKKCLHLGEVGQGARMKLVVNMIMGQMMTALGEGMALGRNCGLDGGQLLEVLDAGAMANPMFKGKGQMLLSGEFPTSFPLKHMQKDLRLAVELGDRLGQPLHGAATANESFKRARAAGHADEDFAAVFRVLE-   -
               SCOP domains d3pdua1 A:1-163 automated matches                                                                                                                                  d3pdua2 A:164-287 automated matches                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhh..eeee..hhhhhhhhhhhh.ee..hhhhhhhhh.eeee...hhhhhhhhhhh..hhhhh.....eeee....hhhhhhhhhhhhhhh..eeee..ee.hhhhhhhh.eeeeeeehhhhhhhhhhhhhhheeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pdu A   1 MTTYGFLGLGIMGGPMAANLVRAGFDVTVWNRNPAKCAPLVALGARQASSPAEVCAACDITIAMLADPAAAREVCFGANGVLEGIGGGRGYIDMSTVDDETSTAIGAAVTARGGRFLEAPVSGTKKPAEDGTLIILAAGDQSLFTDAGPAFAALGKKCLHLGEVGQGARMKLVVNMIMGQMMTALGEGMALGRNCGLDGGQLLEVLDAGAMANPMFKGKGQMLLSGEFPTSFPLKHMQKDLRLAVELGDRLGQPLHGAATANESFKRARAAGHADEDFAAVFRVLEA 287
                                    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       


Chain B from PDB  Type:PROTEIN  Length:286
 aligned with Q74DE4_GEOSL | Q74DE4 from UniProtKB/TrEMBL  Length:286

    Alignment length:286
                                                                                                                                                                                                                                                                                                                      286 
                                    11        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       281    | 
         Q74DE4_GEOSL     2 TTYGFLGLGIMGGPMAANLVRAGFDVTVWNRNPAKCAPLVALGARQASSPAEVCAACDITIAMLADPAAAREVCFGANGVLEGIGGGRGYIDMSTVDDETSTAIGAAVTARGGRFLEAPVSGTKKPAEDGTLIILAAGDQSLFTDAGPAFAALGKKCLHLGEVGQGARMKLVVNMIMGQMMTALGEGMALGRNCGLDGGQLLEVLDAGAMANPMFKGKGQMLLSGEFPTSFPLKHMQKDLRLAVELGDRLGQPLHGAATANESFKRARAAGHADEDFAAVFRVLE-   -
               SCOP domains d3pdub1 B:2-163 automated matches                                                                                                                                 d3pdub2 B:164-287 automated matches                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhh..eeeee..hhhhhhhhhhhh.ee..hhhhhhhhh.eeee...hhhhhhhhhhh..hhhhh.....eeee....hhhhhhhhhhhhhhh..eeee..ee.hhhhhhhh.eeeeeeehhhhhhhhhhhhhhheeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pdu B   2 TTYGFLGLGIMGGPMAANLVRAGFDVTVWNRNPAKCAPLVALGARQASSPAEVCAACDITIAMLADPAAAREVCFGANGVLEGIGGGRGYIDMSTVDDETSTAIGAAVTARGGRFLEAPVSGTKKPAEDGTLIILAAGDQSLFTDAGPAFAALGKKCLHLGEVGQGARMKLVVNMIMGQMMTALGEGMALGRNCGLDGGQLLEVLDAGAMANPMFKGKGQMLLSGEFPTSFPLKHMQKDLRLAVELGDRLGQPLHGAATANESFKRARAAGHADEDFAAVFRVLEA 287
                                    11        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       281      


Chain C from PDB  Type:PROTEIN  Length:286
 aligned with Q74DE4_GEOSL | Q74DE4 from UniProtKB/TrEMBL  Length:286

    Alignment length:286
                                                                                                                                                                                                                                                                                                                      286 
                                    11        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       281    | 
         Q74DE4_GEOSL     2 TTYGFLGLGIMGGPMAANLVRAGFDVTVWNRNPAKCAPLVALGARQASSPAEVCAACDITIAMLADPAAAREVCFGANGVLEGIGGGRGYIDMSTVDDETSTAIGAAVTARGGRFLEAPVSGTKKPAEDGTLIILAAGDQSLFTDAGPAFAALGKKCLHLGEVGQGARMKLVVNMIMGQMMTALGEGMALGRNCGLDGGQLLEVLDAGAMANPMFKGKGQMLLSGEFPTSFPLKHMQKDLRLAVELGDRLGQPLHGAATANESFKRARAAGHADEDFAAVFRVLE-   -
               SCOP domains d3pduc1 C:2-163 automated matches                                                                                                                                 d3pduc2 C:164-287 automated matches                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhh..eeeee..hhhhhhhhhhhh.ee..hhhhhhhhh.eeee...hhhhhhhhhhh..hhhhh.....eeee....hhhhhhhhhhhhhhh..eeee..ee.hhhhhhhh.eeeeeeehhhhhhhhhhhhhhheeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pdu C   2 TTYGFLGLGIMGGPMAANLVRAGFDVTVWNRNPAKCAPLVALGARQASSPAEVCAACDITIAMLADPAAAREVCFGANGVLEGIGGGRGYIDMSTVDDETSTAIGAAVTARGGRFLEAPVSGTKKPAEDGTLIILAAGDQSLFTDAGPAFAALGKKCLHLGEVGQGARMKLVVNMIMGQMMTALGEGMALGRNCGLDGGQLLEVLDAGAMANPMFKGKGQMLLSGEFPTSFPLKHMQKDLRLAVELGDRLGQPLHGAATANESFKRARAAGHADEDFAAVFRVLEA 287
                                    11        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       281      


Chain D from PDB  Type:PROTEIN  Length:287
 aligned with Q74DE4_GEOSL | Q74DE4 from UniProtKB/TrEMBL  Length:286

    Alignment length:287
                                                                                                                                                                                                                                                                                                                       286 
                                    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     | 
         Q74DE4_GEOSL     1 MTTYGFLGLGIMGGPMAANLVRAGFDVTVWNRNPAKCAPLVALGARQASSPAEVCAACDITIAMLADPAAAREVCFGANGVLEGIGGGRGYIDMSTVDDETSTAIGAAVTARGGRFLEAPVSGTKKPAEDGTLIILAAGDQSLFTDAGPAFAALGKKCLHLGEVGQGARMKLVVNMIMGQMMTALGEGMALGRNCGLDGGQLLEVLDAGAMANPMFKGKGQMLLSGEFPTSFPLKHMQKDLRLAVELGDRLGQPLHGAATANESFKRARAAGHADEDFAAVFRVLE-   -
               SCOP domains d3pdud1 D:1-163 automated matches                                                                                                                                  d3pdud2 D:164-287 automated matches                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhh..eeee..hhhhhhhhhhhh.ee..hhhhhhhhh.eeee...hhhhhhhhhhh..hhhhh.....eeee....hhhhhhhhhhhhhhh..eeee..ee.hhhhhhhh.eeeeeeehhhhhhhhhhhhhhheeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pdu D   1 MTTYGFLGLGIMGGPMAANLVRAGFDVTVWNRNPAKCAPLVALGARQASSPAEVCAACDITIAMLADPAAAREVCFGANGVLEGIGGGRGYIDMSTVDDETSTAIGAAVTARGGRFLEAPVSGTKKPAEDGTLIILAAGDQSLFTDAGPAFAALGKKCLHLGEVGQGARMKLVVNMIMGQMMTALGEGMALGRNCGLDGGQLLEVLDAGAMANPMFKGKGQMLLSGEFPTSFPLKHMQKDLRLAVELGDRLGQPLHGAATANESFKRARAAGHADEDFAAVFRVLEA 287
                                    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       


Chain E from PDB  Type:PROTEIN  Length:287
 aligned with Q74DE4_GEOSL | Q74DE4 from UniProtKB/TrEMBL  Length:286

    Alignment length:287
                                                                                                                                                                                                                                                                                                                       286 
                                    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     | 
         Q74DE4_GEOSL     1 MTTYGFLGLGIMGGPMAANLVRAGFDVTVWNRNPAKCAPLVALGARQASSPAEVCAACDITIAMLADPAAAREVCFGANGVLEGIGGGRGYIDMSTVDDETSTAIGAAVTARGGRFLEAPVSGTKKPAEDGTLIILAAGDQSLFTDAGPAFAALGKKCLHLGEVGQGARMKLVVNMIMGQMMTALGEGMALGRNCGLDGGQLLEVLDAGAMANPMFKGKGQMLLSGEFPTSFPLKHMQKDLRLAVELGDRLGQPLHGAATANESFKRARAAGHADEDFAAVFRVLE-   -
               SCOP domains d3pdue1 E:1-163 automated matches                                                                                                                                  d3pdue2 E:164-287 automated matches                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhh..eeee..hhhhhhhhhhhh.ee..hhhhhhhhh.eeee...hhhhhhhhhhh..hhhhh.....eeee....hhhhhhhhhhhhhhh..eeee..ee.hhhhhhhh.eeeeeeehhhhhhhhhhhhhhheeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pdu E   1 MTTYGFLGLGIMGGPMAANLVRAGFDVTVWNRNPAKCAPLVALGARQASSPAEVCAACDITIAMLADPAAAREVCFGANGVLEGIGGGRGYIDMSTVDDETSTAIGAAVTARGGRFLEAPVSGTKKPAEDGTLIILAAGDQSLFTDAGPAFAALGKKCLHLGEVGQGARMKLVVNMIMGQMMTALGEGMALGRNCGLDGGQLLEVLDAGAMANPMFKGKGQMLLSGEFPTSFPLKHMQKDLRLAVELGDRLGQPLHGAATANESFKRARAAGHADEDFAAVFRVLEA 287
                                    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       


Chain F from PDB  Type:PROTEIN  Length:286
 aligned with Q74DE4_GEOSL | Q74DE4 from UniProtKB/TrEMBL  Length:286

    Alignment length:286
                                                                                                                                                                                                                                                                                                                      286 
                                    11        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       281    | 
         Q74DE4_GEOSL     2 TTYGFLGLGIMGGPMAANLVRAGFDVTVWNRNPAKCAPLVALGARQASSPAEVCAACDITIAMLADPAAAREVCFGANGVLEGIGGGRGYIDMSTVDDETSTAIGAAVTARGGRFLEAPVSGTKKPAEDGTLIILAAGDQSLFTDAGPAFAALGKKCLHLGEVGQGARMKLVVNMIMGQMMTALGEGMALGRNCGLDGGQLLEVLDAGAMANPMFKGKGQMLLSGEFPTSFPLKHMQKDLRLAVELGDRLGQPLHGAATANESFKRARAAGHADEDFAAVFRVLE-   -
               SCOP domains d3pduf1 F:2-163 automated matches                                                                                                                                 d3pduf2 F:164-287 automated matches                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhh...eeee..hhhhhhhhhhhh.ee..hhhhhhhhh.eeee...hhhhhhhhhhh..hhhhhh....eeee....hhhhhhhhhhhhhhh..eeee..ee.hhhhhhhh.eeeeeeehhhhhhhhhhhhhhheeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pdu F   2 TTYGFLGLGIMGGPMAANLVRAGFDVTVWNRNPAKCAPLVALGARQASSPAEVCAACDITIAMLADPAAAREVCFGANGVLEGIGGGRGYIDMSTVDDETSTAIGAAVTARGGRFLEAPVSGTKKPAEDGTLIILAAGDQSLFTDAGPAFAALGKKCLHLGEVGQGARMKLVVNMIMGQMMTALGEGMALGRNCGLDGGQLLEVLDAGAMANPMFKGKGQMLLSGEFPTSFPLKHMQKDLRLAVELGDRLGQPLHGAATANESFKRARAAGHADEDFAAVFRVLEA 287
                                    11        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       281      


Chain G from PDB  Type:PROTEIN  Length:284
 aligned with Q74DE4_GEOSL | Q74DE4 from UniProtKB/TrEMBL  Length:286

    Alignment length:284
                                    12        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       272       282    
         Q74DE4_GEOSL     3 TYGFLGLGIMGGPMAANLVRAGFDVTVWNRNPAKCAPLVALGARQASSPAEVCAACDITIAMLADPAAAREVCFGANGVLEGIGGGRGYIDMSTVDDETSTAIGAAVTARGGRFLEAPVSGTKKPAEDGTLIILAAGDQSLFTDAGPAFAALGKKCLHLGEVGQGARMKLVVNMIMGQMMTALGEGMALGRNCGLDGGQLLEVLDAGAMANPMFKGKGQMLLSGEFPTSFPLKHMQKDLRLAVELGDRLGQPLHGAATANESFKRARAAGHADEDFAAVFRVLE 286
               SCOP domains d3pdug1 G:3-163 automated matches                                                                                                                                d3pdug2 G:164-286 automated matches                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhhhh...eeee..hhhhhhhhhhhh.ee..hhhhhhhhh.eeee...hhhhhhhhhhh..hhhhhh....eeee....hhhhhhhhhhhhhhh..eeee..ee.hhhhhhhh.eeeeeeehhhhhhhhhhhhhhheeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pdu G   3 TYGFLGLGIMGGPMAANLVRAGFDVTVWNRNPAKCAPLVALGARQASSPAEVCAACDITIAMLADPAAAREVCFGANGVLEGIGGGRGYIDMSTVDDETSTAIGAAVTARGGRFLEAPVSGTKKPAEDGTLIILAAGDQSLFTDAGPAFAALGKKCLHLGEVGQGARMKLVVNMIMGQMMTALGEGMALGRNCGLDGGQLLEVLDAGAMANPMFKGKGQMLLSGEFPTSFPLKHMQKDLRLAVELGDRLGQPLHGAATANESFKRARAAGHADEDFAAVFRVLE 286
                                    12        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       272       282    


Chain H from PDB  Type:PROTEIN  Length:286
 aligned with Q74DE4_GEOSL | Q74DE4 from UniProtKB/TrEMBL  Length:286

    Alignment length:286
                                                                                                                                                                                                                                                                                                                      286 
                                    11        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       281    | 
         Q74DE4_GEOSL     2 TTYGFLGLGIMGGPMAANLVRAGFDVTVWNRNPAKCAPLVALGARQASSPAEVCAACDITIAMLADPAAAREVCFGANGVLEGIGGGRGYIDMSTVDDETSTAIGAAVTARGGRFLEAPVSGTKKPAEDGTLIILAAGDQSLFTDAGPAFAALGKKCLHLGEVGQGARMKLVVNMIMGQMMTALGEGMALGRNCGLDGGQLLEVLDAGAMANPMFKGKGQMLLSGEFPTSFPLKHMQKDLRLAVELGDRLGQPLHGAATANESFKRARAAGHADEDFAAVFRVLE-   -
               SCOP domains d3pduh1 H:2-163 automated matches                                                                                                                                 d3pduh2 H:164-287 automated matches                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhh..eeeee..hhhhhhhhhhhh.ee..hhhhhhhhh.eeee...hhhhhhhhhhh..hhhhhh....eeee....hhhhhhhhhhhhhhh..eeee..ee.hhhhhhhh.eeeeeeehhhhhhhhhhhhhhheeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pdu H   2 TTYGFLGLGIMGGPMAANLVRAGFDVTVWNRNPAKCAPLVALGARQASSPAEVCAACDITIAMLADPAAAREVCFGANGVLEGIGGGRGYIDMSTVDDETSTAIGAAVTARGGRFLEAPVSGTKKPAEDGTLIILAAGDQSLFTDAGPAFAALGKKCLHLGEVGQGARMKLVVNMIMGQMMTALGEGMALGRNCGLDGGQLLEVLDAGAMANPMFKGKGQMLLSGEFPTSFPLKHMQKDLRLAVELGDRLGQPLHGAATANESFKRARAAGHADEDFAAVFRVLEA 287
                                    11        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       281
   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, 16)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3PDU)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H   (Q74DE4_GEOSL | Q74DE4)
molecular function
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004616    phosphogluconate dehydrogenase (decarboxylating) activity    Catalysis of the reaction: 6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH + H+.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3pdu)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3pdu
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q74DE4_GEOSL | Q74DE4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q74DE4_GEOSL | Q74DE4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3PDU)

(-) Related Entries Specified in the PDB File

3pef