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(-) Description

Title :  HUMAN GAR TFASE COMPLEX STRUCTURE WITH POLYGLUTAMATED 10-(TRIFLUOROACETYL)-5,10-DIDEAZAACYCLIC-5,6,7,8-TETRAHYDROFOLIC ACID
 
Authors :  Y. Zhang, J. Desharnais, D. L. Boger, I. A. Wilson
Date :  03 Nov 03  (Deposition) - 14 Jun 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Protein-Cofactor Analogue Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Zhang, J. Desharnais, D. L. Boger, I. A. Wilson
Human Gar Tfase Complex Structure
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
    ChainsA, B
    EC Number2.1.2.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22A
    Expression System StrainBL21(DE3)GOLD
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Fragment(RESIDUES 808-1010)
    GenePURN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsPART OF TRIFUNCTIONAL PURINE BIOSYNTHETIC PROTEIN ADENOSINE-3
    SynonymGART

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1KT52Ligand/IonN-{4-4-(2,4-DIAMINO-6-OXO-1,6-DIHYDRO-PYRIMIDIN-5-YL)-1-(2,2,2-TRIFLUORO-1,1-DIHYDROXY-ETHYL)-BUT-2-YL-BENZOYL}-GAMMA-GLUTAMYL-GAMMA-GLUTAMYL-GAMMA-GLUTAMYL-GAMMA-GLUTAMYL-GLUTAMIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1KT51Ligand/IonN-{4-4-(2,4-DIAMINO-6-OXO-1,6-DIHYDRO-PYRIMIDIN-5-YL)-1-(2,2,2-TRIFLUORO-1,1-DIHYDROXY-ETHYL)-BUT-2-YL-BENZOYL}-GAMMA-GLUTAMYL-GAMMA-GLUTAMYL-GAMMA-GLUTAMYL-GAMMA-GLUTAMYL-GLUTAMIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1KT51Ligand/IonN-{4-4-(2,4-DIAMINO-6-OXO-1,6-DIHYDRO-PYRIMIDIN-5-YL)-1-(2,2,2-TRIFLUORO-1,1-DIHYDROXY-ETHYL)-BUT-2-YL-BENZOYL}-GAMMA-GLUTAMYL-GAMMA-GLUTAMYL-GAMMA-GLUTAMYL-GAMMA-GLUTAMYL-GLUTAMIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:64 , MET A:89 , ARG A:90 , ILE A:91 , LEU A:92 , ASN A:106 , HIS A:108 , PRO A:109 , GLY A:117 , SER A:118 , VAL A:139 , ALA A:140 , GLU A:141 , VAL A:143 , ASP A:144 , HOH A:538 , HOH A:572BINDING SITE FOR RESIDUE KT5 A 510
2AC2SOFTWAREARG B:64 , MET B:89 , ARG B:90 , ILE B:91 , LEU B:92 , VAL B:97 , ASN B:106 , HIS B:108 , PRO B:109 , GLY B:117 , SER B:118 , VAL B:139 , ALA B:140 , GLU B:141 , VAL B:143 , ASP B:144 , HOH B:613 , HOH B:620 , HOH B:641 , HOH B:657 , HOH B:666 , HOH B:684 , HOH B:702BINDING SITE FOR RESIDUE KT5 B 610

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RC0)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:112 -Pro A:113
2Leu B:112 -Pro B:113

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RC0)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GARTPS00373 Phosphoribosylglycinamide formyltransferase active site.PUR2_HUMAN940-963
 
  2A:133-156
B:133-156
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GARTPS00373 Phosphoribosylglycinamide formyltransferase active site.PUR2_HUMAN940-963
 
  1A:133-156
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GARTPS00373 Phosphoribosylglycinamide formyltransferase active site.PUR2_HUMAN940-963
 
  1-
B:133-156

(-) Exons   (5, 10)

Asymmetric Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000003818392bENSE00001490224chr21:34915167-34914966202PUR2_HUMAN-00--
1.4aENST000003818394aENSE00002148759chr21:34911662-34911477186PUR2_HUMAN1-49490--
1.5ENST000003818395ENSE00001043425chr21:34907626-3490753196PUR2_HUMAN49-81330--
1.6bENST000003818396bENSE00002174056chr21:34907059-34906885175PUR2_HUMAN81-139590--
1.7aENST000003818397aENSE00001043434chr21:34904762-34904651112PUR2_HUMAN139-176380--
1.8aENST000003818398aENSE00001043411chr21:34903863-3490379569PUR2_HUMAN177-199230--
1.9cENST000003818399cENSE00002197902chr21:34903190-34903065126PUR2_HUMAN200-241420--
1.11ENST0000038183911ENSE00001751727chr21:34901243-3490115688PUR2_HUMAN242-271300--
1.12cENST0000038183912cENSE00001753916chr21:34900910-3490082586PUR2_HUMAN271-299290--
1.12fENST0000038183912fENSE00001621771chr21:34900641-34900473169PUR2_HUMAN300-356570--
1.13aENST0000038183913aENSE00001777765chr21:34897307-34897076232PUR2_HUMAN356-433780--
1.14bENST0000038183914bENSE00001646436chr21:34894589-3489449595PUR2_HUMAN433-465330--
1.15ENST0000038183915ENSE00001653663chr21:34893322-34893213110PUR2_HUMAN465-501370--
1.16bENST0000038183916bENSE00001638032chr21:34892869-34892671199PUR2_HUMAN502-568670--
1.17ENST0000038183917ENSE00001683013chr21:34889915-34889664252PUR2_HUMAN568-652850--
1.18ENST0000038183918ENSE00001681935chr21:34889448-34889296153PUR2_HUMAN652-703520--
1.19aENST0000038183919aENSE00001696316chr21:34883765-34883559207PUR2_HUMAN703-772700--
1.20bENST0000038183920bENSE00001689617chr21:34882227-34882090138PUR2_HUMAN772-818472A:1-11
B:1-11
11
11
1.21bENST0000038183921bENSE00001632330chr21:34878411-34878281131PUR2_HUMAN818-861442A:11-54
B:11-54
44
44
1.22ENST0000038183922ENSE00001656872chr21:34878009-34877868142PUR2_HUMAN862-909482A:55-102
B:55-102
48
48
1.23ENST0000038183923ENSE00001636975chr21:34876834-34876719116PUR2_HUMAN909-947392A:102-140
B:102-140
39
39
1.24bENST0000038183924bENSE00001736479chr21:34876622-34876238385PUR2_HUMAN948-1010632A:141-200
B:141-200
60
60

(-) 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:200
 aligned with PUR2_HUMAN | P22102 from UniProtKB/Swiss-Prot  Length:1010

    Alignment length:200
                                   817       827       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1007
          PUR2_HUMAN    808 ARVAVLISGTGSNLQALIDSTREPNSSAQIDIVISNKAAVAGLDKAERAGIPTRVINHKLYKNRVEFDSAIDLVLEEFSIDIVCLAGFMRILSGPFVQKWNGKMLNIHPSLLPSFKGSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVKRGDTVATLSERVKLAEHKIFPAALQLVASGTVQLGENGKICWV 1007
               SCOP domains d1rc0a_ A: Glycinamide ribonucleotide transformylase, GART                                                                                                                                               SCOP domains
               CATH domains 1rc0A00 A:1-200  [code=3.40.50.170, no name defined]                                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhh......eeeeeee....hhhhhhhhhh...eee.hhhhh.hhhhhhhhhhhhhhhh...eeee.......hhhhhhhh...eeeee..........hhhhhhhhhh..eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eee.....eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------GART  PDB: A:133-156    -------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.20b -------------------------------------------Exon 1.22  PDB: A:55-102 UniProt: 862-909       --------------------------------------Exon 1.24b  PDB: A:141-200 UniProt: 948-1010 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.21b  PDB: A:11-54 UniProt: 818-861   -----------------------------------------------Exon 1.23  PDB: A:102-140              ------------------------------------------------------------ Transcript 1 (2)
                1rc0 A    1 ARVAVLISGTGSNLQALIDSTREPNSSAQIDIVISNKAAVAGLDKAERAGIPTRVINHKLYKNRVEFDSAIDLVLEEFSIDIVCLAGFMRILSGPFVQKWNGKMLNIHPSLLPSFKGSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVKRGDTVATLSERVKLAEHKIFPAALQLVASGTVQLGENGKICWV  200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain B from PDB  Type:PROTEIN  Length:200
 aligned with PUR2_HUMAN | P22102 from UniProtKB/Swiss-Prot  Length:1010

    Alignment length:200
                                   817       827       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1007
          PUR2_HUMAN    808 ARVAVLISGTGSNLQALIDSTREPNSSAQIDIVISNKAAVAGLDKAERAGIPTRVINHKLYKNRVEFDSAIDLVLEEFSIDIVCLAGFMRILSGPFVQKWNGKMLNIHPSLLPSFKGSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVKRGDTVATLSERVKLAEHKIFPAALQLVASGTVQLGENGKICWV 1007
               SCOP domains d1rc0b_ B: Glycinamide ribonucleotide transformylase, GART                                                                                                                                               SCOP domains
               CATH domains 1rc0B00 B:1-200  [code=3.40.50.170, no name defined]                                                                                                                                                     CATH domains
           Pfam domains (1) Formyl_trans_N-1rc0B01 B:1-181                                                                                                                                                       ------------------- Pfam domains (1)
           Pfam domains (2) Formyl_trans_N-1rc0B02 B:1-181                                                                                                                                                       ------------------- Pfam domains (2)
         Sec.struct. author .eeeeee...hhhhhhhhhhhh......eeeeeee....hhhhhhhhhh...eee.hhhhh.hhhhhhhhhhhhhhhh...eeee.......hhhhhhhh...eeeee..........hhhhhhhhhh..eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eee.....eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------GART  PDB: B:133-156    -------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.20b -------------------------------------------Exon 1.22  PDB: B:55-102 UniProt: 862-909       --------------------------------------Exon 1.24b  PDB: B:141-200 UniProt: 948-1010 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.21b  PDB: B:11-54 UniProt: 818-861   -----------------------------------------------Exon 1.23  PDB: B:102-140              ------------------------------------------------------------ Transcript 1 (2)
                1rc0 B    1 ARVAVLISGTGSNLQALIDSTREPNSSAQIDIVISNKAAVAGLDKAERAGIPTRVINHKLYKNRVEFDSAIDLVLEEFSIDIVCLAGFMRILSGPFVQKWNGKMLNIHPSLLPSFKGSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVKRGDTVATLSERVKLAEHKIFPAALQLVASGTVQLGENGKICWV  200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

   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 Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (27, 27)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PUR2_HUMAN | P22102)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0016742    hydroxymethyl-, formyl- and related transferase activity    Catalysis of the transfer of a hydroxymethyl- or formyl group from one compound (donor) to another (acceptor).
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004637    phosphoribosylamine-glycine ligase activity    Catalysis of the reaction: 5-phospho-D-ribosylamine + ATP + glycine = N(1)-(5-phospho-D-ribosyl)glycinamide + ADP + 2 H(+) + phosphate.
    GO:0004641    phosphoribosylformylglycinamidine cyclo-ligase activity    Catalysis of the reaction: 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine + ATP = 5-amino-1-(5-phospho-D-ribosyl)imidazole + ADP + 2 H(+) + phosphate.
    GO:0004644    phosphoribosylglycinamide formyltransferase activity    Catalysis of the reaction: 10-formyltetrahydrofolate + N1-(5-phospho-D-ribosyl)glycinamide = tetrahydrofolate + N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide.
    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:0006189    'de novo' IMP biosynthetic process    The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate, by the stepwise assembly of a purine ring on ribose 5-phosphate.
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0003360    brainstem development    The progression of the brainstem from its formation to the mature structure. The brainstem is the part of the brain that connects the brain with the spinal cord.
    GO:0021549    cerebellum development    The process whose specific outcome is the progression of the cerebellum over time, from its formation to the mature structure. The cerebellum is the portion of the brain in the back of the head between the cerebrum and the pons. In mice, the cerebellum controls balance for walking and standing, modulates the force and range of movement and is involved in the learning of motor skills.
    GO:0021987    cerebral cortex development    The progression of the cerebral cortex over time from its initial formation until its mature state. The cerebral cortex is the outer layered region of the telencephalon.
    GO:0006544    glycine metabolic process    The chemical reactions and pathways involving glycine, aminoethanoic acid.
    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:0009113    purine nucleobase biosynthetic process    The chemical reactions and pathways resulting in the formation of purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.
    GO:0006164    purine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    GO:0009168    purine ribonucleoside monophosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of purine ribonucleoside monophosphate, a compound consisting of a purine base linked to a ribose sugar esterified with phosphate on the sugar.
    GO:0010035    response to inorganic substance    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 an inorganic substance stimulus.
    GO:0010033    response to organic substance    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 an organic substance stimulus.
    GO:0009156    ribonucleoside monophosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of a ribonucleoside monophosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with phosphate on the sugar.
    GO:0046654    tetrahydrofolate biosynthetic process    The chemical reactions and pathways resulting in the formation of tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PUR2_HUMAN | P221021mej 1men 1meo 1njs 1rbm 1rbq 1rby 1rbz 1rc1 1zlx 1zly 2qk4 2v9y 4ew1 4ew2 4ew3 4zyt 4zyu 4zyv 4zyw 4zyx 4zyy 4zyz 4zz0 4zz1 4zz2 4zz3 5j9f

(-) Related Entries Specified in the PDB File

1mej APO HUMAN GAR TFASE STRUCTURE AT PH 8.5
1meo APO HUMAN GAR TFASE STRUCTURE AT PH 4.2
1njs HUMAN GAR TFASE COMPLEX STRUCTURE WITH 10-(TRIFLUOROACETYL) -5,10-DIDEAZAACYCLIC-5,6,7,8-TETRAHYDROFOLIC ACID AT PHYSIOLOGICAL PH
1rbm
1rbq
1rby
1rbz
1rc1