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
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)

(-) Description

Title :  STRUCTURAL MECHANISM OF ENZYME MISTARGETING IN HEREDITARY KIDNEY STONE DISEASE IN VITRO
 
Authors :  X. Zhang, S. Djordjevic, M. Bartlam, S. Ye, Z. Rao, C. J. Danpure
Date :  30 Oct 02  (Deposition) - 11 Nov 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Transferase, Aminotransferase, Pyridoxal Phosphate (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Djordjevic, X. Zhang, M. Bartlam, S. Ye, Z. Rao, C. J. Danpure
Structural Implications Of A G170R Mutation Of Alanine:Glyoxylate Aminotransferase That Is Associated With Peroxisome-To-Mitochondrion Mistargeting.
Acta Crystallogr. , Sect. F V. 66 233 2010
PubMed-ID: 20208150  |  Reference-DOI: 10.1107/S1744309109054645

(-) Compounds

Molecule 1 - ALANINE--GLYOXYLATE AMINOTRANSFERASE
    ChainsA
    EC Number2.6.1.51, 2.6.1.44
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSERINE--PYRUVATE AMINOTRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1AOA1Ligand/Ion(AMINOOXY)ACETIC ACID
2GOL7Ligand/IonGLYCEROL
3LLP1Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1AOA1Ligand/Ion(AMINOOXY)ACETIC ACID
2GOL7Ligand/IonGLYCEROL
3LLP1Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
Biological Unit 2 (3, 18)
No.NameCountTypeFull Name
1AOA2Ligand/Ion(AMINOOXY)ACETIC ACID
2GOL14Ligand/IonGLYCEROL
3LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:28 , GLY A:29 , LLP A:209 , MET A:348 , ARG A:360BINDING SITE FOR RESIDUE AOA A 1001
2AC2SOFTWARELEU A:24 , ARG A:71 , ASP A:196 , PHE A:343BINDING SITE FOR RESIDUE GOL A 1002
3AC3SOFTWARELYS A:228 , GLN A:290 , ARG A:370 , GLU A:371BINDING SITE FOR RESIDUE GOL A 1003
4AC4SOFTWARESER A:19 , ASP A:52 , GLN A:55 , GLU A:59BINDING SITE FOR RESIDUE GOL A 1004
5AC5SOFTWAREGLN A:110 , ARG A:111 , TRP A:246BINDING SITE FOR RESIDUE GOL A 1006
6AC6SOFTWARELEU A:278BINDING SITE FOR RESIDUE GOL A 1007
7AC7SOFTWARELEU A:7 , ASN A:22 , ARG A:170 , ASP A:196BINDING SITE FOR RESIDUE GOL A 1008
8AC8SOFTWAREGLN A:137 , GLU A:138 , GLU A:141BINDING SITE FOR RESIDUE GOL A 1009

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J04)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:29 -Pro A:30

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (49, 49)

Asymmetric Unit (49, 49)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_060547T9NSPYA_HUMANPolymorphism115014558AT9N
02UniProtVAR_000587P11LSPYA_HUMANPolymorphism34116584AP11L
03UniProtVAR_048236N22SSPYA_HUMANPolymorphism34885252AN22S
04UniProtVAR_074582R36CSPYA_HUMANDisease (HP1)180177157AR36C
05UniProtVAR_074583G41ESPYA_HUMANDisease (HP1)180177168AG41E
06UniProtVAR_000588G41RSPYA_HUMANDisease (HP1)121908523AG41R
07UniProtVAR_010969G41VSPYA_HUMANDisease (HP1)180177168AG41V
08UniProtVAR_074584G47RSPYA_HUMANDisease (HP1)180177173AG47R
09UniProtVAR_008878G82ESPYA_HUMANDisease (HP1)121908522AG82E
10UniProtVAR_060548G82RSPYA_HUMANDisease (HP1)180177185AG82R
11UniProtVAR_060549W108RSPYA_HUMANDisease (HP1)180177197AW108R
12UniProtVAR_060550A112DSPYA_HUMANDisease (HP1)796052061AA112D
13UniProtVAR_010971G116RSPYA_HUMANDisease (HP1)180177207AG116R
14UniProtVAR_074585L150PSPYA_HUMANDisease (HP1)180177222AL150P
15UniProtVAR_000589F152ISPYA_HUMANDisease (HP1)121908524AF152I
16UniProtVAR_060552L153VSPYA_HUMANDisease (HP1)180177223AL153V
17UniProtVAR_010972G156RSPYA_HUMANDisease (HP1)121908530AG156R
18UniProtVAR_060553S158LSPYA_HUMANDisease (HP1)180177225AS158L
19UniProtVAR_074586G161CSPYA_HUMANDisease (HP1)180177227AG161C
20UniProtVAR_060554G161RSPYA_HUMANDisease (HP1)180177227AG161R
21UniProtVAR_074587G161SSPYA_HUMANDisease (HP1)180177227AG161S
22UniProtVAR_074588L166PSPYA_HUMANDisease (HP1)180177230AL166P
23UniProtVAR_000590G170RSPYA_HUMANDisease (HP1)121908529AR170R
24UniProtVAR_060555C173YSPYA_HUMANDisease (HP1)180177231AC173Y
25UniProtVAR_010973D183NSPYA_HUMANDisease (HP1)180177236AD183N
26UniProtVAR_000591S187FSPYA_HUMANDisease (HP1)180177238AS187F
27UniProtVAR_060556G190RSPYA_HUMANDisease (HP1)180177239AG190R
28UniProtVAR_060557M195RSPYA_HUMANDisease (HP1)180177244AM195R
29UniProtVAR_060558D201ESPYA_HUMANDisease (HP1)180177246AD201E
30UniProtVAR_074589I202NSPYA_HUMANUnclassified (HP1)  ---AI202N
31UniProtVAR_000592S205PSPYA_HUMANDisease (HP1)121908520AS205P
32UniProtVAR_060559S218LSPYA_HUMANDisease (HP1)180177253AS218L
33UniProtVAR_008879R233CSPYA_HUMANDisease (HP1)121908526AR233C
34UniProtVAR_008880R233HSPYA_HUMANDisease (HP1)121908527AR233H
35UniProtVAR_060560R233LSPYA_HUMANDisease (HP1)121908527AR233L
36UniProtVAR_060561D243HSPYA_HUMANDisease (HP1)180177258AD243H
37UniProtVAR_008881I244TSPYA_HUMANDisease (HP1)121908525AI244T
38UniProtVAR_060562C253RSPYA_HUMANDisease (HP1)180177264AC253R
39UniProtVAR_060563I279MSPYA_HUMANDisease (HP1)180177277AI279M
40UniProtVAR_060564I279TSPYA_HUMANPolymorphism140992177AI279T
41UniProtVAR_060565A280VSPYA_HUMANPolymorphism73106685AA280V
42UniProtVAR_060566S287TSPYA_HUMANDisease (HP1)180177289AS287T
43UniProtVAR_060567R289CSPYA_HUMANDisease (HP1)180177290AR289C
44UniProtVAR_048237A295TSPYA_HUMANPolymorphism13408961AA295T
45UniProtVAR_060569L298PSPYA_HUMANDisease (HP1)180177293AL298P
46UniProtVAR_060570V326ISPYA_HUMANPolymorphism115057148AV326I
47UniProtVAR_060571V336DSPYA_HUMANDisease (HP1)180177155AV336D
48UniProtVAR_000593I340MSPYA_HUMANPolymorphism4426527AI340M
49UniProtVAR_060572G350DSPYA_HUMANDisease (HP1)180177156AG350D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (49, 49)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_060547T9NSPYA_HUMANPolymorphism115014558AT9N
02UniProtVAR_000587P11LSPYA_HUMANPolymorphism34116584AP11L
03UniProtVAR_048236N22SSPYA_HUMANPolymorphism34885252AN22S
04UniProtVAR_074582R36CSPYA_HUMANDisease (HP1)180177157AR36C
05UniProtVAR_074583G41ESPYA_HUMANDisease (HP1)180177168AG41E
06UniProtVAR_000588G41RSPYA_HUMANDisease (HP1)121908523AG41R
07UniProtVAR_010969G41VSPYA_HUMANDisease (HP1)180177168AG41V
08UniProtVAR_074584G47RSPYA_HUMANDisease (HP1)180177173AG47R
09UniProtVAR_008878G82ESPYA_HUMANDisease (HP1)121908522AG82E
10UniProtVAR_060548G82RSPYA_HUMANDisease (HP1)180177185AG82R
11UniProtVAR_060549W108RSPYA_HUMANDisease (HP1)180177197AW108R
12UniProtVAR_060550A112DSPYA_HUMANDisease (HP1)796052061AA112D
13UniProtVAR_010971G116RSPYA_HUMANDisease (HP1)180177207AG116R
14UniProtVAR_074585L150PSPYA_HUMANDisease (HP1)180177222AL150P
15UniProtVAR_000589F152ISPYA_HUMANDisease (HP1)121908524AF152I
16UniProtVAR_060552L153VSPYA_HUMANDisease (HP1)180177223AL153V
17UniProtVAR_010972G156RSPYA_HUMANDisease (HP1)121908530AG156R
18UniProtVAR_060553S158LSPYA_HUMANDisease (HP1)180177225AS158L
19UniProtVAR_074586G161CSPYA_HUMANDisease (HP1)180177227AG161C
20UniProtVAR_060554G161RSPYA_HUMANDisease (HP1)180177227AG161R
21UniProtVAR_074587G161SSPYA_HUMANDisease (HP1)180177227AG161S
22UniProtVAR_074588L166PSPYA_HUMANDisease (HP1)180177230AL166P
23UniProtVAR_000590G170RSPYA_HUMANDisease (HP1)121908529AR170R
24UniProtVAR_060555C173YSPYA_HUMANDisease (HP1)180177231AC173Y
25UniProtVAR_010973D183NSPYA_HUMANDisease (HP1)180177236AD183N
26UniProtVAR_000591S187FSPYA_HUMANDisease (HP1)180177238AS187F
27UniProtVAR_060556G190RSPYA_HUMANDisease (HP1)180177239AG190R
28UniProtVAR_060557M195RSPYA_HUMANDisease (HP1)180177244AM195R
29UniProtVAR_060558D201ESPYA_HUMANDisease (HP1)180177246AD201E
30UniProtVAR_074589I202NSPYA_HUMANUnclassified (HP1)  ---AI202N
31UniProtVAR_000592S205PSPYA_HUMANDisease (HP1)121908520AS205P
32UniProtVAR_060559S218LSPYA_HUMANDisease (HP1)180177253AS218L
33UniProtVAR_008879R233CSPYA_HUMANDisease (HP1)121908526AR233C
34UniProtVAR_008880R233HSPYA_HUMANDisease (HP1)121908527AR233H
35UniProtVAR_060560R233LSPYA_HUMANDisease (HP1)121908527AR233L
36UniProtVAR_060561D243HSPYA_HUMANDisease (HP1)180177258AD243H
37UniProtVAR_008881I244TSPYA_HUMANDisease (HP1)121908525AI244T
38UniProtVAR_060562C253RSPYA_HUMANDisease (HP1)180177264AC253R
39UniProtVAR_060563I279MSPYA_HUMANDisease (HP1)180177277AI279M
40UniProtVAR_060564I279TSPYA_HUMANPolymorphism140992177AI279T
41UniProtVAR_060565A280VSPYA_HUMANPolymorphism73106685AA280V
42UniProtVAR_060566S287TSPYA_HUMANDisease (HP1)180177289AS287T
43UniProtVAR_060567R289CSPYA_HUMANDisease (HP1)180177290AR289C
44UniProtVAR_048237A295TSPYA_HUMANPolymorphism13408961AA295T
45UniProtVAR_060569L298PSPYA_HUMANDisease (HP1)180177293AL298P
46UniProtVAR_060570V326ISPYA_HUMANPolymorphism115057148AV326I
47UniProtVAR_060571V336DSPYA_HUMANDisease (HP1)180177155AV336D
48UniProtVAR_000593I340MSPYA_HUMANPolymorphism4426527AI340M
49UniProtVAR_060572G350DSPYA_HUMANDisease (HP1)180177156AG350D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (49, 98)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_060547T9NSPYA_HUMANPolymorphism115014558AT9N
02UniProtVAR_000587P11LSPYA_HUMANPolymorphism34116584AP11L
03UniProtVAR_048236N22SSPYA_HUMANPolymorphism34885252AN22S
04UniProtVAR_074582R36CSPYA_HUMANDisease (HP1)180177157AR36C
05UniProtVAR_074583G41ESPYA_HUMANDisease (HP1)180177168AG41E
06UniProtVAR_000588G41RSPYA_HUMANDisease (HP1)121908523AG41R
07UniProtVAR_010969G41VSPYA_HUMANDisease (HP1)180177168AG41V
08UniProtVAR_074584G47RSPYA_HUMANDisease (HP1)180177173AG47R
09UniProtVAR_008878G82ESPYA_HUMANDisease (HP1)121908522AG82E
10UniProtVAR_060548G82RSPYA_HUMANDisease (HP1)180177185AG82R
11UniProtVAR_060549W108RSPYA_HUMANDisease (HP1)180177197AW108R
12UniProtVAR_060550A112DSPYA_HUMANDisease (HP1)796052061AA112D
13UniProtVAR_010971G116RSPYA_HUMANDisease (HP1)180177207AG116R
14UniProtVAR_074585L150PSPYA_HUMANDisease (HP1)180177222AL150P
15UniProtVAR_000589F152ISPYA_HUMANDisease (HP1)121908524AF152I
16UniProtVAR_060552L153VSPYA_HUMANDisease (HP1)180177223AL153V
17UniProtVAR_010972G156RSPYA_HUMANDisease (HP1)121908530AG156R
18UniProtVAR_060553S158LSPYA_HUMANDisease (HP1)180177225AS158L
19UniProtVAR_074586G161CSPYA_HUMANDisease (HP1)180177227AG161C
20UniProtVAR_060554G161RSPYA_HUMANDisease (HP1)180177227AG161R
21UniProtVAR_074587G161SSPYA_HUMANDisease (HP1)180177227AG161S
22UniProtVAR_074588L166PSPYA_HUMANDisease (HP1)180177230AL166P
23UniProtVAR_000590G170RSPYA_HUMANDisease (HP1)121908529AR170R
24UniProtVAR_060555C173YSPYA_HUMANDisease (HP1)180177231AC173Y
25UniProtVAR_010973D183NSPYA_HUMANDisease (HP1)180177236AD183N
26UniProtVAR_000591S187FSPYA_HUMANDisease (HP1)180177238AS187F
27UniProtVAR_060556G190RSPYA_HUMANDisease (HP1)180177239AG190R
28UniProtVAR_060557M195RSPYA_HUMANDisease (HP1)180177244AM195R
29UniProtVAR_060558D201ESPYA_HUMANDisease (HP1)180177246AD201E
30UniProtVAR_074589I202NSPYA_HUMANUnclassified (HP1)  ---AI202N
31UniProtVAR_000592S205PSPYA_HUMANDisease (HP1)121908520AS205P
32UniProtVAR_060559S218LSPYA_HUMANDisease (HP1)180177253AS218L
33UniProtVAR_008879R233CSPYA_HUMANDisease (HP1)121908526AR233C
34UniProtVAR_008880R233HSPYA_HUMANDisease (HP1)121908527AR233H
35UniProtVAR_060560R233LSPYA_HUMANDisease (HP1)121908527AR233L
36UniProtVAR_060561D243HSPYA_HUMANDisease (HP1)180177258AD243H
37UniProtVAR_008881I244TSPYA_HUMANDisease (HP1)121908525AI244T
38UniProtVAR_060562C253RSPYA_HUMANDisease (HP1)180177264AC253R
39UniProtVAR_060563I279MSPYA_HUMANDisease (HP1)180177277AI279M
40UniProtVAR_060564I279TSPYA_HUMANPolymorphism140992177AI279T
41UniProtVAR_060565A280VSPYA_HUMANPolymorphism73106685AA280V
42UniProtVAR_060566S287TSPYA_HUMANDisease (HP1)180177289AS287T
43UniProtVAR_060567R289CSPYA_HUMANDisease (HP1)180177290AR289C
44UniProtVAR_048237A295TSPYA_HUMANPolymorphism13408961AA295T
45UniProtVAR_060569L298PSPYA_HUMANDisease (HP1)180177293AL298P
46UniProtVAR_060570V326ISPYA_HUMANPolymorphism115057148AV326I
47UniProtVAR_060571V336DSPYA_HUMANDisease (HP1)180177155AV336D
48UniProtVAR_000593I340MSPYA_HUMANPolymorphism4426527AI340M
49UniProtVAR_060572G350DSPYA_HUMANDisease (HP1)180177156AG350D

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_5PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site.SPYA_HUMAN200-220  1A:200-220
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_5PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site.SPYA_HUMAN200-220  1A:200-220
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_5PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site.SPYA_HUMAN200-220  2A:200-220

(-) Exons   (11, 11)

Asymmetric Unit (11, 11)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003075031aENSE00001843474chr2:241807896-241808447552SPYA_HUMAN1-55551A:4-5552
1.2ENST000003075032ENSE00001162366chr2:241808587-241808779193SPYA_HUMAN56-120651A:56-12065
1.3ENST000003075033ENSE00001162358chr2:241810061-24181012565SPYA_HUMAN120-141221A:120-14122
1.4bENST000003075034bENSE00001162348chr2:241810766-241810866101SPYA_HUMAN142-175341A:142-17534
1.5aENST000003075035aENSE00001162341chr2:241812396-24181246671SPYA_HUMAN175-199251A:175-19925
1.6ENST000003075036ENSE00001162333chr2:241813395-24181347985SPYA_HUMAN199-227291A:199-22729
1.7ENST000003075037ENSE00001162328chr2:241814526-24181462196SPYA_HUMAN227-259331A:227-25933
1.8aENST000003075038aENSE00001162322chr2:241815352-24181542170SPYA_HUMAN259-282241A:259-28224
1.9bENST000003075039bENSE00001162318chr2:241816954-24181704996SPYA_HUMAN283-314321A:283-31432
1.10ENST0000030750310ENSE00001162312chr2:241817439-241817567129SPYA_HUMAN315-357431A:315-35743
1.11aENST0000030750311aENSE00001895938chr2:241818131-241818537407SPYA_HUMAN358-392351A:358-39033

(-) 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:387
 aligned with SPYA_HUMAN | P21549 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:387
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       
           SPYA_HUMAN     4 HKLLVTPPKALLKPLSIPNQLLLGPGPSNLPPRIMAAGGLQMIGSMSKDMYQIMDEIKEGIQYVFQTRNPLTLVISGSGHCALEAALVNVLEPGDSFLVGANGIWGQRAVDIGERIGARVHPMTKDPGGHYTLQEVEEGLAQHKPVLLFLTHGESSTGVLQPLDGFGELCHRYKCLLLVDSVASLGGTPLYMDRQGIDILYSGSQKALNAPPGTSLISFSDKAKKKMYSRKTKPFSFYLDIKWLANFWGCDDQPRMYHHTIPVISLYSLRESLALIAEQGLENSWRQHREAAAYLHGRLQALGLQLFVKDPALRLPTVTTVAVPAGYDWRDIVSYVIDHFDIEIMGGLGPSTGKVLRIGLLGCNATRENVDRVTEALRAALQHCPKK 390
               SCOP domains d1j04a_ A: Alanine-glyoxylate aminotransferase                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1j04A01 A:4-33,A:283-390      1j04A02 A:34-282 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                     1j04A01 A:4-33,A:283-390 Aspartate Aminotransferase, domain 1                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh.......ee........hhhhhhhh........hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhh.....eee...hhhhhhhhhhhhhh...eee.........hhhhhhhhhhhhh..eeeee.............hhhhhhhh...eeeee..................eeeee...........eeeeehhhhhhhhhhh.........hhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............eeeee.....hhhhhhhhhhhhhhee....hhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
             SAPs(SNPs) (1) -----N-L----------S-------------C----E-----R----------------------------------E-------------------------R---D---R---------------------------------P-IV--R-L--C----P---R--Y---------N---F--R----R-----EN--P------------L--------------C---------HT--------R-------------------------MV------T-C-----T--P---------------------------I---------D---M---------D---------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------R----------------------------------------R------------------------------------------------------------------------------R-----------------------------------------------------------------------H---------------------------------------------T--------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) -------------------------------------V-----------------------------------------------------------------------------------------------------------------------S-----------------------------------------------------------------------L------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_5  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:4-55 UniProt: 1-55 [INCOMPLETE]   Exon 1.2  PDB: A:56-120 UniProt: 56-120                          ---------------------Exon 1.4b  PDB: A:142-175         -----------------------Exon 1.6  PDB: A:199-227     -------------------------------Exon 1.8a  PDB: A:259-28Exon 1.9b  PDB: A:283-314       Exon 1.10  PDB: A:315-357 UniProt: 315-357 Exon 1.11a  PDB: A:358-390        Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------------------Exon 1.3              ---------------------------------Exon 1.5a  PDB: A:175-199---------------------------Exon 1.7  PDB: A:227-259         ----------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1j04 A   4 HKLLVTPPKALLKPLSIPNQLLLGPGPSNLPPRIMAAGGLQMIGSMSKDMYQIMDEIKEGIQYVFQTRNPLTLVISGSGHCALEAALVNVLEPGDSFLVGANGIWGQRAVDIGERIGARVHPMTKDPGGHYTLQEVEEGLAQHKPVLLFLTHGESSTGVLQPLDGFRELCHRYKCLLLVDSVASLGGTPLYMDRQGIDILYSGSQkALNAPPGTSLISFSDKAKKKMYSRKTKPFSFYLDIKWLANFWGCDDQPRMYHHTIPVISLYSLRESLALIAEQGLENSWRQHREAAAYLHGRLQALGLQLFVKDPALRLPTVTTVAVPAGYDWRDIVSYVIDHFDIEIMGGLGPSTGKVLRIGLLGCNATRENVDRVTEALRAALQHCPKK 390
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203     | 213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       
                                                                                                                                                                                                                                       209-LLP                                                                                                                                                                                 

   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  (0, 0)

(no "Pfam Domain" information available for 1J04)

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)
Chain A   (SPYA_HUMAN | P21549)
molecular function
    GO:0008453    alanine-glyoxylate transaminase activity    Catalysis of the reaction: L-alanine + glyoxylate = pyruvate + glycine.
    GO:0016597    amino acid binding    Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0043621    protein self-association    Interacting selectively and non-covalently with a domain within the same polypeptide.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0004760    serine-pyruvate transaminase activity    Catalysis of the reaction: L-serine + pyruvate = 3-hydroxypyruvate + L-alanine.
    GO:0008483    transaminase activity    Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0042853    L-alanine catabolic process    The chemical reactions and pathways resulting in the breakdown of L-alanine, the L-enantiomer of 2-aminopropanoic acid, i.e. (2S)-2-aminopropanoic acid.
    GO:0019448    L-cysteine catabolic process    The chemical reactions and pathways resulting in the breakdown of L-cysteine, the L-enantiomer of 2-amino-3-mercaptopropanoic acid, i.e. (2R)-2-amino-3-mercaptopropanoic acid.
    GO:0007219    Notch signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0019265    glycine biosynthetic process, by transamination of glyoxylate    The chemical reactions and pathways resulting in the formation of glycine by the transamination of glyoxylate.
    GO:0009436    glyoxylate catabolic process    The chemical reactions and pathways resulting in the breakdown of glyoxylate, the anion of glyoxylic acid, HOC-COOH.
    GO:0046487    glyoxylate metabolic process    The chemical reactions and pathways involving glyoxylate, the anion of glyoxylic acid, HOC-COOH.
    GO:0046724    oxalic acid secretion    The controlled release of oxalic acid, ethanedioic acid, by a cell or a tissue.
    GO:0010498    proteasomal protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds that is mediated by the proteasome.
    GO:0042866    pyruvate biosynthetic process    The chemical reactions and pathways resulting in the formation of pyruvate, 2-oxopropanoate.
    GO:0051591    response to cAMP    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 cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
    GO:0051384    response to glucocorticoid    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 glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
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:0005782    peroxisomal matrix    The volume contained within the membranes of a peroxisome; in many cells the matrix contains a crystalloid core largely composed of urate oxidase.
    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.

 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
    AOA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    LLP  [ 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 ]
 
  Cis Peptide Bonds
    Gly A:29 - Pro A:30   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1j04
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SPYA_HUMAN | P21549
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.6.1.44
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
  2.6.1.51
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  259900
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  SPYA_HUMAN | P21549
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SPYA_HUMAN | P215491h0c 2yob 3r9a 4cbr 4cbs 4i8a 4kxk 4kyo 5f9s 5hhy

(-) Related Entries Specified in the PDB File

1h0c 1H0C CONTAINS THE STRUCTURE OF NORMAL AGT