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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE OXIDIZED FORM OF HUMAN SSADH
 
Authors :  Y. -G. Kim, K. -J. Kim
Date :  19 Jan 09  (Deposition) - 09 Jun 09  (Release) - 24 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Mitochondrion, Oxidoreductase, Transit Peptide, Disease Mutation, Ssa, Nad, Polymorphism, Mitochondria (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. -G. Kim, S. Lee, O. -S. Kwon, S. -Y. Park, S. -J. Lee, B. -J. Park, K. -J. Kim
Redox-Switch Modulation Of Human Ssadh By Dynamic Catalytic Loop.
Embo J. V. 28 959 2009
PubMed-ID: 19300440  |  Reference-DOI: 10.1038/EMBOJ.2009.40

(-) Compounds

Molecule 1 - SUCCINATE-SEMIALDEHYDE DEHYDROGENASE, MITOCHONDRIAL
    ChainsA
    EC Number1.2.1.24
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE30
    Expression System StrainM15(PREP4)
    Expression System Taxid562
    FragmentRESIDUES 49-535
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNAD(+)-DEPENDENT SUCCINIC SEMIALDEHYDE DEHYDROGENASE, ALDEHYDE DEHYDROGENASE FAMILY 5 MEMBER A1, SUCCINIC SEMIALDEHYDE DEHYDROGENASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (4x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION
Biological Unit 1 (1, 32)
No.NameCountTypeFull Name
1SO432Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:368 , ARG A:369 , VAL A:370 , HIS A:413BINDING SITE FOR RESIDUE SO4 A1536
2AC2SOFTWAREGLN A:349 , THR A:451 , GLU A:452 , HOH A:2249BINDING SITE FOR RESIDUE SO4 A1537
3AC3SOFTWAREGLY A:67 , ARG A:68 , TRP A:69 , HOH A:2022BINDING SITE FOR RESIDUE SO4 A1538
4AC4SOFTWARESER A:251BINDING SITE FOR RESIDUE SO4 A1539
5AC5SOFTWAREARG A:103 , GLU A:386 , HOH A:2292 , HOH A:2293BINDING SITE FOR RESIDUE SO4 A1540
6AC6SOFTWARETHR A:408 , GLY A:409 , HOH A:2294BINDING SITE FOR RESIDUE SO4 A1541
7AC7SOFTWAREARG A:68 , SER A:83 , ALA A:85 , HOH A:2295BINDING SITE FOR RESIDUE SO4 A1542
8AC8SOFTWAREHOH A:2296 , HOH A:2298 , HOH A:2299BINDING SITE FOR RESIDUE SO4 A1543

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:340 -A:342

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2W8N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (17, 17)

Asymmetric Unit (17, 17)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_026199C93FSSDH_HUMANDisease (SSADHD)765561257AC93F
02UniProtVAR_026200G176RSSDH_HUMANDisease (SSADHD)72552281AG176R
03UniProtVAR_016758H180YSSDH_HUMANPolymorphism2760118AH180Y
04UniProtVAR_016759P182LSSDH_HUMANPolymorphism3765310AP182L
05UniProtVAR_026201C223YSSDH_HUMANDisease (SSADHD)72552282AC223Y
06UniProtVAR_026202T233MSSDH_HUMANDisease (SSADHD)  ---AT233M
07UniProtVAR_026228A237SSSDH_HUMANPolymorphism62621664AA237S
08UniProtVAR_026203N255SSSDH_HUMANDisease (SSADHD)145087265AN255S
09UniProtVAR_026204G268ESSDH_HUMANDisease (SSADHD)375628463AG268E
10UniProtVAR_026205N335KSSDH_HUMANDisease (SSADHD)72552283AN335K
11UniProtVAR_069047N372SSSDH_HUMANPolymorphism  ---AN372S
12UniProtVAR_026206P382LSSDH_HUMANDisease (SSADHD)  ---AP382L
13UniProtVAR_026207P382QSSDH_HUMANDisease (SSADHD)  ---AP382Q
14UniProtVAR_026229V406ISSDH_HUMANPolymorphism143741652AV406I
15UniProtVAR_026208G409DSSDH_HUMANDisease (SSADHD)118203984AG409D
16UniProtVAR_026209V487ESSDH_HUMANDisease (SSADHD)  ---AV487E
17UniProtVAR_026210G533RSSDH_HUMANDisease (SSADHD)72552284AG533R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (17, 68)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_026199C93FSSDH_HUMANDisease (SSADHD)765561257AC93F
02UniProtVAR_026200G176RSSDH_HUMANDisease (SSADHD)72552281AG176R
03UniProtVAR_016758H180YSSDH_HUMANPolymorphism2760118AH180Y
04UniProtVAR_016759P182LSSDH_HUMANPolymorphism3765310AP182L
05UniProtVAR_026201C223YSSDH_HUMANDisease (SSADHD)72552282AC223Y
06UniProtVAR_026202T233MSSDH_HUMANDisease (SSADHD)  ---AT233M
07UniProtVAR_026228A237SSSDH_HUMANPolymorphism62621664AA237S
08UniProtVAR_026203N255SSSDH_HUMANDisease (SSADHD)145087265AN255S
09UniProtVAR_026204G268ESSDH_HUMANDisease (SSADHD)375628463AG268E
10UniProtVAR_026205N335KSSDH_HUMANDisease (SSADHD)72552283AN335K
11UniProtVAR_069047N372SSSDH_HUMANPolymorphism  ---AN372S
12UniProtVAR_026206P382LSSDH_HUMANDisease (SSADHD)  ---AP382L
13UniProtVAR_026207P382QSSDH_HUMANDisease (SSADHD)  ---AP382Q
14UniProtVAR_026229V406ISSDH_HUMANPolymorphism143741652AV406I
15UniProtVAR_026208G409DSSDH_HUMANDisease (SSADHD)118203984AG409D
16UniProtVAR_026209V487ESSDH_HUMANDisease (SSADHD)  ---AV487E
17UniProtVAR_026210G533RSSDH_HUMANDisease (SSADHD)72552284AG533R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALDEHYDE_DEHYDR_GLUPS00687 Aldehyde dehydrogenases glutamic acid active site.SSDH_HUMAN305-312  1A:305-312
2ALDEHYDE_DEHYDR_CYSPS00070 Aldehyde dehydrogenases cysteine active site.SSDH_HUMAN333-344  1A:333-344
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALDEHYDE_DEHYDR_GLUPS00687 Aldehyde dehydrogenases glutamic acid active site.SSDH_HUMAN305-312  4A:305-312
2ALDEHYDE_DEHYDR_CYSPS00070 Aldehyde dehydrogenases cysteine active site.SSDH_HUMAN333-344  4A:333-344

(-) Exons   (0, 0)

(no "Exon" information available for 2W8N)

(-) 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:480
 aligned with SSDH_HUMAN | P51649 from UniProtKB/Swiss-Prot  Length:535

    Alignment length:480
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535
           SSDH_HUMAN    56 AALLRTDSFVGGRWLPAAATFPVQDPASGAALGMVADCGVREARAAVRAAYEAFCRWREVSAKERSSLLRKWYNLMIQNKDDLARIITAESGKPLKEAHGEILYSAFFLEWFSEEARRVYGDIIHTPAKDRRALVLKQPIGVAAVITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPFSALALAELASQAGIPSGVYNVIPCSRKNAKEVGEAICTDPLVSKISFTGSTTTGKILLHHAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNTGQTCVCSNQFLVQRGIHDAFVKAFAEAMKKNLRVGNGFEEGTTQGPLINEKAVEKVEKQVNDAVSKGATVVTGGKRHQLGKNFFEPTLLCNVTQDMLCTHEETFGPLAPVIKFDTEEEAIAIANAADVGLAGYFYSQDPAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLELKYVCYGGL 535
               SCOP domains d2w8na_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2w8nA01 A:56-308,A:500-535 Aldehyde Dehydrogenase; Chain A, domain 1                                                                                                                                                                                         2w8nA02 A:309-499 Aldehyde Dehydrogenase; Chain A, domain 2                                                                                                                                    2w8nA01 A:56-308,A:500-535           CATH domains
               Pfam domains -------------Aldedh-2w8nA01 A:69-530                                                                                                                                                                                                                                                                                                                                                                                                                                                       ----- Pfam domains
         Sec.struct. author .......eee..eee....eeeee......eeeeee..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..eee.......eeeeeeee..eeeee......hhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhh.....eee...hhhhhhhhhhhhh....eeeeeeeehhhhhhhhhhhhhh...eeeeee.eeeeeee....hhhhhhhhhhhhhh........eeeeeeeehhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhh...eeee..............eeeeeehhhhhh........eeeeeee.hhhhhhhhhh......eeeee..hhhhhhhhhhhh...eeee..............hhh.ee......hhhhh.eeeeeeee... Sec.struct. author
             SAPs(SNPs) (1) -------------------------------------F----------------------------------------------------------------------------------R---Y-L----------------------------------------Y---------M---S-----------------S------------E------------------------------------------------------------------K------------------------------------S---------L-----------------------I--D-----------------------------------------------------------------------------E---------------------------------------------R-- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Q--------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ALDEHYDE--------------------ALDEHYDE_DEH----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2w8n A  56 AALLRTDSFVGGRWLPAAATFPVQDPASGAALGMVADCGVREARAAVRAAYEAFCRWREVSAKERSSLLRKWYNLMIQNKDDLARIITAESGKPLKEAHGEILYSAFFLEWFSEEARRVYGDIIHTPAKDRRALVLKQPIGVAAVITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPFSALALAELASQAGIPSGVYNVIPCSRKNAKEVGEAICTDPLVSKISFTGSTTTGKILLHHAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNTGQTCVCSNQFLVQRGIHDAFVKAFAEAMKKNLRVGNGFEEGTTQGPLINEKAVEKVEKQVNDAVSKGATVVTGGKRHQLGKNFFEPTLLCNVTQDMLCTHEETFGPLAPVIKFDTEEEAIAIANAADVGLAGYFYSQDPAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLELKYVCYGGL 535
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535

   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, 1)

Asymmetric Unit

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (29, 29)

Asymmetric Unit(hide GO term definitions)
Chain A   (SSDH_HUMAN | P51649)
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:0004029    aldehyde dehydrogenase (NAD) activity    Catalysis of the reaction: an aldehyde + NAD+ + H2O = an acid + NADH + H+.
    GO:0031406    carboxylic acid binding    Interacting selectively and non-covalently with a carboxylic acid, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
    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:0016620    oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0004777    succinate-semialdehyde dehydrogenase (NAD+) activity    Catalysis of the reaction: succinate semialdehyde + NAD+ + H2O = succinate + NADH + H+.
    GO:0009013    succinate-semialdehyde dehydrogenase [NAD(P)+] activity    Catalysis of the reaction: succinate semialdehyde + NAD(P)+ + H2O = succinate + NAD(P)H + H+.
biological process
    GO:0006083    acetate metabolic process    The chemical reactions and pathways involving acetate, the anion of acetic acid.
    GO:0007417    central nervous system development    The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
    GO:0006681    galactosylceramide metabolic process    The chemical reactions and pathways involving galactosylceramides, any compound formed by the replacement of the glycosidic hydroxyl group of a cyclic form of galactose by a ceramide group.
    GO:0009450    gamma-aminobutyric acid catabolic process    The chemical reactions and pathways resulting in the breakdown of gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms.
    GO:0009448    gamma-aminobutyric acid metabolic process    The chemical reactions and pathways involving gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms.
    GO:0006006    glucose metabolic process    The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
    GO:0006678    glucosylceramide metabolic process    The chemical reactions and pathways involving glucosylceramides, any compound formed by the replacement of the glycosidic hydroxyl group of a cyclic form of glucose by a ceramide group. They are neutral glycolipids containing equimolar amounts of fatty acid, glucose, and sphingosine or a sphingosine derivative.
    GO:0006536    glutamate metabolic process    The chemical reactions and pathways involving glutamate, the anion of 2-aminopentanedioic acid.
    GO:0006541    glutamine metabolic process    The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid.
    GO:0006749    glutathione metabolic process    The chemical reactions and pathways involving glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide (H2O2) and oxidized ascorbate, and it participates in the gamma-glutamyl cycle.
    GO:0006650    glycerophospholipid metabolic process    The chemical reactions and pathways involving glycerophospholipids, any derivative of glycerophosphate that contains at least one O-acyl, O-alkyl, or O-alkenyl group attached to the glycerol residue.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0042135    neurotransmitter catabolic process    The chemical reactions and pathways resulting in the breakdown of any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell.
    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.
    GO:0009791    post-embryonic development    The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
    GO:0022904    respiratory electron transport chain    A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0046459    short-chain fatty acid metabolic process    The chemical reactions and pathways involving fatty acids with a chain length of less than C6.
    GO:0006105    succinate metabolic process    The chemical reactions and pathways involving succinate, also known as butanedioate or ethane dicarboxylate, the dianion of succinic acid. Succinate is an important intermediate in metabolism and a component of the TCA cycle.
cellular component
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SSDH_HUMAN | P516492w8o 2w8p 2w8q 2w8r

(-) Related Entries Specified in the PDB File

2w8o THE CRYSTAL STRUCTURE OF THE REDUCED FORM OF HUMAN SSADH
2w8p THE CRYSTAL STRUCTURE OF HUMAN C340A SSADH
2w8q THE CRYSTAL STRUCTURE OF HUMAN SSADH IN COMPLEX WITH SSA.
2w8r THE CRYSTAL STRUCTURE OF HUMAN SSADH IN COMPLEX WITH NAD+