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(-) Description

Title :  HUMAN BRAIN ASPARTOACYLASE COMPLEX WITH INTERMEDIATE ANALOG (N-PHOSPHONOMETHYL-L-ASPARTATE)
 
Authors :  J. Le Coq, A. Pavlovsky, R. Sanishvili, R. E. Viola
Date :  04 Dec 06  (Deposition) - 06 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Canavan Disease, N-Acetyl-L-Aspartate, Zinc-Dependent Hydrolase, Aspartoacylase Family, Hydrolase, Aminoacylase-2, Acy2, Aspa, N- Phosphonomethyl-L-Aspartate (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Le Coq, A. Pavlovsky, R. Malik, R. Sanishvili, C. Xu, R. E. Viola
Examination Of The Mechanism Of Human Brain Aspartoacylase Through The Binding Of An Intermediate Analogue.
Biochemistry V. 47 3484 2008
PubMed-ID: 18293939  |  Reference-DOI: 10.1021/BI702400X

(-) Compounds

Molecule 1 - ASPARTOACYLASE
    ChainsA, B
    EC Number3.5.1.15
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System PlasmidPPICZA
    Expression System StrainKM71H
    Expression System Taxid4922
    Expression System Vector TypePLASMID
    GeneASPA, ACY2, ASP
    OrganBRAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAMINOACYLASE-2, ACY-2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1AS92Ligand/IonN-[HYDROXY(METHYL)PHOSPHORYL]-L-ASPARTIC ACID
2ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:21 , GLU A:24 , HIS A:116 , AS9 A:501BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREHIS B:21 , GLU B:24 , HIS B:116 , AS9 B:501BINDING SITE FOR RESIDUE ZN B 401
3AC3SOFTWAREHIS A:21 , GLU A:24 , ARG A:63 , ASN A:70 , ARG A:71 , HIS A:116 , ASN A:117 , ILE A:127 , TYR A:164 , ARG A:168 , GLU A:178 , GLU A:285 , TYR A:288 , ZN A:401BINDING SITE FOR RESIDUE AS9 A 501
4AC4SOFTWAREHIS B:21 , GLU B:24 , ARG B:63 , ASN B:70 , ARG B:71 , HIS B:116 , ASN B:117 , TYR B:164 , ARG B:168 , GLU B:178 , GLU B:285 , TYR B:288 , ZN B:401BINDING SITE FOR RESIDUE AS9 B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O4H)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Gly A:101 -Pro A:102
2Ala A:148 -Pro A:149
3Glu A:158 -His A:159
4Gly A:180 -Pro A:181
5Gly B:101 -Pro B:102
6Ala B:148 -Pro B:149
7Gly B:180 -Pro B:181
8Asp B:266 -Gly B:267

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (43, 86)

Asymmetric/Biological Unit (43, 86)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_039079I16TACY2_HUMANDisease (CAND)769653717A/BI16T
02UniProtVAR_016778H21PACY2_HUMANDisease (CAND)  ---A/BH21P
03UniProtVAR_016782E24GACY2_HUMANDisease (CAND)104894551A/BE24G
04UniProtVAR_078086E24KACY2_HUMANDisease (CAND)  ---A/BE24K
05UniProtVAR_039080G27RACY2_HUMANDisease (CAND)766328537A/BG27R
06UniProtVAR_078087L30PACY2_HUMANDisease (CAND)  ---A/BL30P
07UniProtVAR_016779A57TACY2_HUMANDisease (CAND)  ---A/BA57T
08UniProtVAR_078088A57VACY2_HUMANDisease (CAND)  ---A/BA57V
09UniProtVAR_078089R63TACY2_HUMANDisease (CAND)  ---A/BR63T
10UniProtVAR_016783D68AACY2_HUMANDisease (CAND)  ---A/BD68A
11UniProtVAR_078090L69RACY2_HUMANDisease (CAND)776777887A/BL69R
12UniProtVAR_078091G101VACY2_HUMANDisease (CAND)  ---A/BG101V
13UniProtVAR_039081D114EACY2_HUMANDisease (CAND)  ---A/BD114E
14UniProtVAR_016784D114YACY2_HUMANDisease (CAND)  ---A/BD114Y
15UniProtVAR_039082G123EACY2_HUMANDisease (CAND)  ---A/BG123E
16UniProtVAR_078092E129KACY2_HUMANDisease (CAND)773049803A/BE129K
17UniProtVAR_004995I143TACY2_HUMANDisease (CAND)777936704A/BI143T
18UniProtVAR_004996C152RACY2_HUMANDisease (CAND)104894548A/BC152R
19UniProtVAR_016785C152WACY2_HUMANDisease (CAND)  ---A/BC152W
20UniProtVAR_039083C152YACY2_HUMANDisease (CAND)  ---A/BC152Y
21UniProtVAR_039084R168CACY2_HUMANDisease (CAND)  ---A/BR168C
22UniProtVAR_016780R168HACY2_HUMANDisease (CAND)770706390A/BR168H
23UniProtVAR_078093I170TACY2_HUMANDisease (CAND)144321760A/BI170T
24UniProtVAR_078094I177TACY2_HUMANDisease (CAND)  ---A/BI177T
25UniProtVAR_078095G180VACY2_HUMANDisease (CAND)  ---A/BG180V
26UniProtVAR_016781P181TACY2_HUMANDisease (CAND)786204572A/BP181T
27UniProtVAR_039085P183HACY2_HUMANDisease (CAND)  ---A/BP183H
28UniProtVAR_039086V186FACY2_HUMANDisease (CAND)  ---A/BV186F
29UniProtVAR_039087M195RACY2_HUMANDisease (CAND)  ---A/BM195R
30UniProtVAR_078096D204HACY2_HUMANDisease (CAND)  ---A/BD204H
31UniProtVAR_016786Y231CACY2_HUMANDisease (CAND)104894550A/BY231C
32UniProtVAR_016787H244RACY2_HUMANDisease (CAND)  ---A/BH244R
33UniProtVAR_078097Q248RACY2_HUMANDisease (CAND)  ---A/BQ248R
34UniProtVAR_016788D249VACY2_HUMANDisease (CAND)104894552A/BD249V
35UniProtVAR_004998G274RACY2_HUMANDisease (CAND)761064915A/BG274R
36UniProtVAR_039088P280LACY2_HUMANDisease (CAND)  ---A/BP280L
37UniProtVAR_039089P280SACY2_HUMANDisease (CAND)750505963A/BP280S
38UniProtVAR_004999E285AACY2_HUMANDisease (CAND)28940279A/BE285A
39UniProtVAR_078098A286DACY2_HUMANDisease (CAND)  ---A/BA286D
40UniProtVAR_039090A287TACY2_HUMANDisease (CAND)774323189A/BA287T
41UniProtVAR_005000F295SACY2_HUMANDisease (CAND)  ---A/BF295S
42UniProtVAR_005001A305EACY2_HUMANDisease (CAND)28940574A/BA305E
43UniProtVAR_039091C310GACY2_HUMANPolymorphism376854191A/BC310G

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2O4H)

(-) Exons   (6, 12)

Asymmetric/Biological Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000002630802aENSE00001116147chr17:3379296-3379689394ACY2_HUMAN1-79792A:10-79
B:10-79
70
70
1.3ENST000002630803ENSE00000669162chr17:3384897-3385092196ACY2_HUMAN79-144662A:79-144
B:79-144
66
66
1.4ENST000002630804ENSE00000669164chr17:3386793-338688694ACY2_HUMAN145-176322A:145-176
B:145-176
32
32
1.5ENST000002630805ENSE00000669166chr17:3392529-3392636108ACY2_HUMAN176-212372A:176-212
B:176-212
37
37
1.6ENST000002630806ENSE00000669168chr17:3397644-3397753110ACY2_HUMAN212-248372A:212-248
B:212-248
37
37
1.7bENST000002630807bENSE00001923034chr17:3402185-34067134529ACY2_HUMAN249-313652A:249-310
B:249-310
62
62

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:301
 aligned with ACY2_HUMAN | P45381 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:301
                                    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 
           ACY2_HUMAN    10 HIQKVAIFGGTHGNELTGVFLVKHWLENGAEIQRTGLEVKPFITNPRAVKKCTRYIDCDLNRIFDLENLGKKMSEDLPYEVRRAQEINHLFGPKDSEDSYDIIFDLHNTTSNMGCTLILEDSRNNFLIQMFHYIKTSLAPLPCYVYLIEHPSLKYATTRSIAKYPVGIEVGPQPQGVLRADILDQMRKMIKHALDFIHHFNEGKEFPPCAIEVYKIIEKVDYPRDENGEIAAIIHPNLQDQDWKPLHPGDPMFLTLDGKTIPLGGDCTVYPVFVNEAAYYEKKEAFAKTTKLTLNAKSIRC 310
               SCOP domains d2o4ha_ A: Aspartoacylase AspA                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhh..hhhhh....eeeeee.hhhhhhhh......hhhhh.hhhhhh.......hhhhhhhhhhhhhhh.........eeeeeee.....eeeeee....hhhhhhhhhhhhhhhh...eeeee.........hhhhhh.eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeeeeeee............ee................eeee.....eee.......eee...hhhhh.....eeeeeeeeeee..... Sec.struct. author
             SAPs(SNPs) (1) ------T----P--G--R--P--------------------------T-----T----AR-------------------------------V------------E--------E-----K-------------T--------R---------------C-T------T--VT-H--F--------R--------H--------------------------C------------R---RV------------------------R-----L----ADT-------S---------E----G SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------K--------------------------------V--------------------------------------------------------Y-------------------------------------W---------------H---------------------------------------------------------------------------------------------------------------S------------------------------ SAPs(SNPs) (2)
             SAPs(SNPs) (3) ----------------------------------------------------------------------------------------------------------------------------------------------Y-------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: A:10-79 UniProt: 1-79 [INCOMPLETE]                    -----------------------------------------------------------------Exon 1.4  PDB: A:145-176        -----------------------------------Exon 1.6  PDB: A:212-248             Exon 1.7b  PDB: A:249-310 UniProt: 249-313 [INCOMPLETE]        Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------Exon 1.3  PDB: A:79-144 UniProt: 79-144                           -------------------------------Exon 1.5  PDB: A:176-212             -------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2o4h A  10 HIQKVAIFGGTHGNELTGVFLVKHWLENGAEIQRTGLEVKPFITNPRAVKKCTRYIDCDLNRIFDLENLGKKMSEDLPYEVRRAQEINHLFGPKDSEDSYDIIFDLHNTTSNMGCTLILEDSRNNFLIQMFHYIKTSLAPLPCYVYLIEHPSLKYATTRSIAKYPVGIEVGPQPQGVLRADILDQMRKMIKHALDFIHHFNEGKEFPPCAIEVYKIIEKVDYPRDENGEIAAIIHPNLQDQDWKPLHPGDPMFLTLDGKTIPLGGDCTVYPVFVNEAAYYEKKEAFAKTTKLTLNAKSIRC 310
                                    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 

Chain B from PDB  Type:PROTEIN  Length:301
 aligned with ACY2_HUMAN | P45381 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:301
                                    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 
           ACY2_HUMAN    10 HIQKVAIFGGTHGNELTGVFLVKHWLENGAEIQRTGLEVKPFITNPRAVKKCTRYIDCDLNRIFDLENLGKKMSEDLPYEVRRAQEINHLFGPKDSEDSYDIIFDLHNTTSNMGCTLILEDSRNNFLIQMFHYIKTSLAPLPCYVYLIEHPSLKYATTRSIAKYPVGIEVGPQPQGVLRADILDQMRKMIKHALDFIHHFNEGKEFPPCAIEVYKIIEKVDYPRDENGEIAAIIHPNLQDQDWKPLHPGDPMFLTLDGKTIPLGGDCTVYPVFVNEAAYYEKKEAFAKTTKLTLNAKSIRC 310
               SCOP domains d2o4hb_ B: Aspartoacylase AspA                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) AstE_AspA-2o4hB01 B:10-301                                                                                                                                                                                                                                                                          --------- Pfam domains (1)
           Pfam domains (2) AstE_AspA-2o4hB02 B:10-301                                                                                                                                                                                                                                                                          --------- Pfam domains (2)
         Sec.struct. author ....eeeee.....hhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhh.......hhhhh.hhhhhh.......hhhhhhhhhhhhhhh.........eeeeeee.....eeeeee....hhhhhhhhhhhhhhhh....eeee.........hhhhhh.eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeeeeeee............ee................eeee.....eee.......eee...hhhhh.....eeeeeeeeeee..... Sec.struct. author
             SAPs(SNPs) (1) ------T----P--G--R--P--------------------------T-----T----AR-------------------------------V------------E--------E-----K-------------T--------R---------------C-T------T--VT-H--F--------R--------H--------------------------C------------R---RV------------------------R-----L----ADT-------S---------E----G SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------K--------------------------------V--------------------------------------------------------Y-------------------------------------W---------------H---------------------------------------------------------------------------------------------------------------S------------------------------ SAPs(SNPs) (2)
             SAPs(SNPs) (3) ----------------------------------------------------------------------------------------------------------------------------------------------Y-------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: B:10-79 UniProt: 1-79 [INCOMPLETE]                    -----------------------------------------------------------------Exon 1.4  PDB: B:145-176        -----------------------------------Exon 1.6  PDB: B:212-248             Exon 1.7b  PDB: B:249-310 UniProt: 249-313 [INCOMPLETE]        Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------Exon 1.3  PDB: B:79-144 UniProt: 79-144                           -------------------------------Exon 1.5  PDB: B:176-212             -------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2o4h B  10 HIQKVAIFGGTHGNELTGVFLVKHWLENGAEIQRTGLEVKPFITNPRAVKKCTRYIDCDLNRIFDLENLGKKMSEDLPYEVRRAQEINHLFGPKDSEDSYDIIFDLHNTTSNMGCTLILEDSRNNFLIQMFHYIKTSLAPLPCYVYLIEHPSLKYATTRSIAKYPVGIEVGPQPQGVLRADILDQMRKMIKHALDFIHHFNEGKEFPPCAIEVYKIIEKVDYPRDENGEIAAIIHPNLQDQDWKPLHPGDPMFLTLDGKTIPLGGDCTVYPVFVNEAAYYEKKEAFAKTTKLTLNAKSIRC 310
                                    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 

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2O4H)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ACY2_HUMAN | P45381)
molecular function
    GO:0004046    aminoacylase activity    Catalysis of the reaction: an N-acyl-L-amino acid + H2O = a carboxylate + an L-amino acid.
    GO:0019807    aspartoacylase activity    Catalysis of the reaction: N-acyl-L-aspartate + H2O = a fatty acid anion + L-aspartate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016811    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides    Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide.
    GO:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006533    aspartate catabolic process    The chemical reactions and pathways resulting in the breakdown of aspartate, the anion derived from aspartic acid, 2-aminobutanedioic acid.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ACY2_HUMAN | P453812i3c 2o53 2q51 4mri 4mxu 4nfr 4tnu

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2O4H)