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(-) Description

Title :  CRYSTAL STRUCTURES OF MEDIUM CHAIN ACYL-COA DEHYDROGENASE FROM PIG LIVER MITOCHONDRIA WITH AND WITHOUT SUBSTRATE
 
Authors :  J. -J. P. Kim, M. Wang, R. Paschke
Date :  13 Jul 94  (Deposition) - 30 Sep 94  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. J. Kim, M. Wang, R. Paschke
Crystal Structures Of Medium-Chain Acyl-Coa Dehydrogenase From Pig Liver Mitochondria With And Without Substrate.
Proc. Natl. Acad. Sci. Usa V. 90 7523 1993
PubMed-ID: 8356049  |  Reference-DOI: 10.1073/PNAS.90.16.7523
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MEDIUM CHAIN ACYL-COA DEHYDROGENASE
    ChainsA, B
    EC Number1.3.99.3
    EngineeredYES
    Organism CommonPIG
    Organism ScientificSUS SCROFA
    Organism Taxid9823

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:133 , VAL A:135 , THR A:136 , GLY A:141 , SER A:142 , TRP A:166 , THR A:168 , ILE A:371 , ILE A:374 , THR A:378 , GLN A:380 , ILE A:384 , HOH A:805 , HOH A:808 , HOH A:809 , HOH A:810 , HOH A:811 , HOH A:985 , ARG B:281 , THR B:283 , PHE B:284 , LEU B:288 , HIS B:291 , GLN B:292 , GLN B:349 , VAL B:350 , GLY B:353BINDING SITE FOR RESIDUE FAD A 399
2AC2SOFTWAREARG A:281 , THR A:283 , PHE A:284 , LEU A:288 , HIS A:291 , GLN A:292 , ILE A:294 , GLN A:349 , VAL A:350 , GLY A:353 , TYR B:133 , VAL B:135 , THR B:136 , GLY B:141 , SER B:142 , TRP B:166 , THR B:168 , ILE B:371 , ILE B:374 , GLU B:376 , THR B:378 , GLN B:380 , HOH B:855 , HOH B:874 , HOH B:904 , HOH B:905 , HOH B:906 , HOH B:907BINDING SITE FOR RESIDUE FAD B 399

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ACYL_COA_DH_1PS00072 Acyl-CoA dehydrogenases signature 1.ACADM_PIG159-171
 
  2A:134-146
B:134-146
2ACYL_COA_DH_2PS00073 Acyl-CoA dehydrogenases signature 2.ACADM_PIG374-393
 
  2A:349-368
B:349-368
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ACYL_COA_DH_1PS00072 Acyl-CoA dehydrogenases signature 1.ACADM_PIG159-171
 
  4A:134-146
B:134-146
2ACYL_COA_DH_2PS00073 Acyl-CoA dehydrogenases signature 2.ACADM_PIG374-393
 
  4A:349-368
B:349-368

(-) Exons   (0, 0)

(no "Exon" information available for 3MDD)

(-) 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:385
 aligned with ACADM_PIG | P41367 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:385
                                    45        55        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     
            ACADM_PIG    36 GFSFELTEQQKEFQATARKFAREEIIPVAAEYDRTGEYPVPLLKRAWELGLMNTHIPESFGGLGLGIIDSCLITEELAYGCTGVQTAIEANTLGQVPLIIGGNYQQQKKYLGRMTEEPLMCAYCVTEPGAGSDVAGIKTKAEKKGDEYIINGQKMWITNGGKANWYFLLARSDPDPKAPASKAFTGFIVEADTPGVQIGRKEINMGQRCSDTRGIVFEDVRVPKENVLTGEGAGFKIAMGTFDKTRPPVAAGAVGLAQRALDEATKYALERKTFGKLLAEHQGISFLLADMAMKVELARLSYQRAAWEIDSGRRNTYYASIAKAYAADIANQLATDAVQVFGGNGFNTEYPVEKLMRDAKIYQIYEGTAQIQRIIIAREHIGRYK 420
               SCOP domains d3mdda2 A:11-241 Medium chain acyl-CoA dehydrogenase, NM domains                                                                                                                                                                       d3mdda1 A:242-395 Medium chain acyl-CoA dehydrogenase, C-domain                                                                                            SCOP domains
               CATH domains 3mddA01 A:11-130 Butyryl-Coa Dehydrogenase, subunit A, domain 1                                                         3mddA02 A:131-251 Butyryl-CoA Dehydrogenase, subunit A, domain 2                                                         3mddA03 A:252-395 Butyryl-CoA Dehydrogenase, subunit A, domain 3                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhh..hhhhhh....hhhhhhhhhhh................hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..eeeeeee.............eeeeee..eeeeeeeee.........eeeeeee............eeeeeee....eeeeeeee.........eeeeeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh.....hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------ACYL_COA_DH_1----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACYL_COA_DH_2       --------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mdd A  11 GFSFELTEQQKEFQATARKFAREEIIPVAAEYDRTGEYPVPLLKRAWELGLMNTHIPESFGGLGLGIIDSCLITEELAYGCTGVQTAIEANTLGQVPLIIGGNYQQQKKYLGRMTEEPLMCAYCVTEPGAGSDVAGIKTKAEKKGDEYIINGQKMWITNGGKANWYFLLARSDPDPKAPASKAFTGFIVEADTPGVQIGRKEINMGQRCSDTRGIVFEDVRVPKENVLTGEGAGFKIAMGTFDKTRPPVAAGAVGLAQRALDEATKYALERKTFGKLLAEHQGISFLLADMAMKVELARLSYQRAAWEIDSGRRNTYYASIAKAYAADIANQLATDAVQVFGGNGFNTEYPVEKLMRDAKIYQIYEGTAQIQRIIIAREHIGRYK 395
                                    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       330       340       350       360       370       380       390     

Chain B from PDB  Type:PROTEIN  Length:385
 aligned with ACADM_PIG | P41367 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:385
                                    45        55        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     
            ACADM_PIG    36 GFSFELTEQQKEFQATARKFAREEIIPVAAEYDRTGEYPVPLLKRAWELGLMNTHIPESFGGLGLGIIDSCLITEELAYGCTGVQTAIEANTLGQVPLIIGGNYQQQKKYLGRMTEEPLMCAYCVTEPGAGSDVAGIKTKAEKKGDEYIINGQKMWITNGGKANWYFLLARSDPDPKAPASKAFTGFIVEADTPGVQIGRKEINMGQRCSDTRGIVFEDVRVPKENVLTGEGAGFKIAMGTFDKTRPPVAAGAVGLAQRALDEATKYALERKTFGKLLAEHQGISFLLADMAMKVELARLSYQRAAWEIDSGRRNTYYASIAKAYAADIANQLATDAVQVFGGNGFNTEYPVEKLMRDAKIYQIYEGTAQIQRIIIAREHIGRYK 420
               SCOP domains d3mddb2 B:11-241 Medium chain acyl-CoA dehydrogenase, NM domains                                                                                                                                                                       d3mddb1 B:242-395 Medium chain acyl-CoA dehydrogenase, C-domain                                                                                            SCOP domains
               CATH domains 3mddB01 B:11-130 Butyryl-Coa Dehydrogenase, subunit A, domain 1                                                         3mddB02 B:131-251 Butyryl-CoA Dehydrogenase, subunit A, domain 2                                                         3mddB03 B:252-395 Butyryl-CoA Dehydrogenase, subunit A, domain 3                                                                                 CATH domains
           Pfam domains (1) ------Acyl-CoA_dh_N-3mddB05 B:17-128                                                                                  ---Acyl-CoA_dh_M-3mddB03 B:132-183                     ----------------------------------------------------------Acyl-CoA_dh_1-3mddB01 B:242-391                                                                                                                       ---- Pfam domains (1)
           Pfam domains (2) ------Acyl-CoA_dh_N-3mddB06 B:17-128                                                                                  ---Acyl-CoA_dh_M-3mddB04 B:132-183                     ----------------------------------------------------------Acyl-CoA_dh_1-3mddB02 B:242-391                                                                                                                       ---- Pfam domains (2)
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhh..hhhhhh....hhhhhhhhhhh................hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..eeeeeee.............eeeeee..eeeeeeeee.........eeeeeee............eeeeeee....eeeeeeee.........eeeeeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh.....hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------ACYL_COA_DH_1----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACYL_COA_DH_2       --------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mdd B  11 GFSFELTEQQKEFQATARKFAREEIIPVAAEYDRTGEYPVPLLKRAWELGLMNTHIPESFGGLGLGIIDSCLITEELAYGCTGVQTAIEANTLGQVPLIIGGNYQQQKKYLGRMTEEPLMCAYCVTEPGAGSDVAGIKTKAEKKGDEYIINGQKMWITNGGKANWYFLLARSDPDPKAPASKAFTGFIVEADTPGVQIGRKEINMGQRCSDTRGIVFEDVRVPKENVLTGEGAGFKIAMGTFDKTRPPVAAGAVGLAQRALDEATKYALERKTFGKLLAEHQGISFLLADMAMKVELARLSYQRAAWEIDSGRRNTYYASIAKAYAADIANQLATDAVQVFGGNGFNTEYPVEKLMRDAKIYQIYEGTAQIQRIIIAREHIGRYK 395
                                    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       330       340       350       360       370       380       390     

   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, 4)

Asymmetric Unit

(-) CATH Domains  (3, 6)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (3, 6)

Asymmetric Unit

(-) Gene Ontology  (30, 30)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ACADM_PIG | P41367)
molecular function
    GO:0003995    acyl-CoA dehydrogenase activity    Catalysis of the reaction: acyl-CoA + acceptor = 2,3-dehydroacyl-CoA + reduced acceptor.
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0000062    fatty-acyl-CoA binding    Interacting selectively and non-covalently with acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with a fatty acyl group.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0070991    medium-chain-acyl-CoA dehydrogenase activity    Catalysis of the reaction: acyl-CoA + acceptor = 2,3-dehydroacyl-CoA + reduced acceptor, where the acyl group is a medium-chain fatty acid residue. A medium chain fatty acid is any fatty acid with a chain length of between C6 and C12.
    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:0016627    oxidoreductase activity, acting on the CH-CH group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
    GO:0052890    oxidoreductase activity, acting on the CH-CH group of donors, with a flavin as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces a flavin.
biological process
    GO:0055007    cardiac muscle cell differentiation    The process in which a cardiac muscle precursor cell acquires specialized features of a cardiac muscle cell. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction.
    GO:0009437    carnitine metabolic process    The chemical reactions and pathways involving carnitine (hydroxy-trimethyl aminobutyric acid), a compound that participates in the transfer of acyl groups across the inner mitochondrial membrane.
    GO:0019254    carnitine metabolic process, CoA-linked    The chemical reactions and pathways involving carnitine, where metabolism is linked to CoA.
    GO:0006635    fatty acid beta-oxidation    A fatty acid oxidation process that results in the complete oxidation of a long-chain fatty acid. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and occurs by successive cycles of reactions during each of which the fatty acid is shortened by a two-carbon fragment removed as acetyl coenzyme A; the cycle continues until only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).
    GO:0033539    fatty acid beta-oxidation using acyl-CoA dehydrogenase    A fatty acid beta-oxidation pathway in which the initial step of each oxidation cycle, which converts an acyl-CoA to a trans-2-enoyl-CoA, is catalyzed by acyl-CoA dehydrogenase; the electrons removed by oxidation pass through the respiratory chain to oxygen and leave H2O as the product. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and ends when only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0005978    glycogen biosynthetic process    The chemical reactions and pathways resulting in the formation of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues.
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0055088    lipid homeostasis    Any process involved in the maintenance of an internal steady state of lipid within an organism or cell.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0001889    liver development    The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
    GO:0051791    medium-chain fatty acid metabolic process    The chemical reactions and pathways involving medium-chain fatty acids, any fatty acid with a chain length of between C6 and C12.
    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:0006082    organic acid metabolic process    The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage.
    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:0006111    regulation of gluconeogenesis    Any process that modulates the frequency, rate or extent of gluconeogenesis, the formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
    GO:0009409    response to cold    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cold stimulus, a temperature stimulus below the optimal temperature for that organism.
    GO:0042594    response to starvation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a starvation stimulus, deprivation of nourishment.
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.
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

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        ACADM_PIG | P413671udy 3mde

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