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(-) Description

Title :  CRYSTAL STRUCTURE OF MGS DOMAIN OF CARBAMOYL-PHOSPHATE SYNTHETASE FROM HOMO SAPIENS
 
Authors :  Y. Xie, Ihsanawati, S. Kishishita, K. Murayama, C. Takemoto, M. Shirozu, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  13 Apr 07  (Deposition) - 15 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Conserved Hypothetical Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Xie, Ihsanawati, S. Kishishita, K. Murayama, C. Takemoto, M. Shirozu, S. Yokoyama
Crystal Structure Of Mgs Domain Of Carbamoyl-Phosphate Synthetase From Homo Sapiens
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CARBAMOYL-PHOSPHATE SYNTHASE
    ChainsA
    EC Number6.3.4.16
    EngineeredYES
    Expression System PlasmidPK060110-54-MD01
    Expression System Vector TypePLASMID
    FragmentMGS DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymCARBAMOYL-PHOSPHATE SYNTHETASE I, CPSASE I

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2YVQ)

(-) Sites  (0, 0)

(no "Site" information available for 2YVQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (13, 13)

Asymmetric Unit (13, 13)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_066137R1371LCPSM_HUMANDisease (CPS1D)  ---AR1371L
02UniProtVAR_017568G1376SCPSM_HUMANPolymorphism140578009AG1376S
03UniProtVAR_066169A1378TCPSM_HUMANDisease (CPS1D)  ---AA1378T
04UniProtVAR_075413L1381SCPSM_HUMANDisease (CPS1D)  ---AL1381S
05UniProtVAR_066138T1391MCPSM_HUMANDisease (CPS1D)  ---AT1391M
06UniProtVAR_066139L1398VCPSM_HUMANDisease (CPS1D)  ---AL1398V
07UniProtVAR_017569T1406NCPSM_HUMANPolymorphism1047891AT1406N
08UniProtVAR_064066P1411LCPSM_HUMANDisease (CPS1D)  ---AP1411L
09UniProtVAR_066140P1439LCPSM_HUMANDisease (CPS1D)  ---AP1439L
10UniProtVAR_066170T1443ACPSM_HUMANDisease (CPS1D)  ---AT1443A
11UniProtVAR_064067R1453QCPSM_HUMANDisease (CPS1D)  ---AR1453Q
12UniProtVAR_064068R1453WCPSM_HUMANDisease (CPS1D)  ---AR1453W
13UniProtVAR_066141P1462RCPSM_HUMANDisease (CPS1D)  ---AP1462R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (13, 13)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_066137R1371LCPSM_HUMANDisease (CPS1D)  ---AR1371L
02UniProtVAR_017568G1376SCPSM_HUMANPolymorphism140578009AG1376S
03UniProtVAR_066169A1378TCPSM_HUMANDisease (CPS1D)  ---AA1378T
04UniProtVAR_075413L1381SCPSM_HUMANDisease (CPS1D)  ---AL1381S
05UniProtVAR_066138T1391MCPSM_HUMANDisease (CPS1D)  ---AT1391M
06UniProtVAR_066139L1398VCPSM_HUMANDisease (CPS1D)  ---AL1398V
07UniProtVAR_017569T1406NCPSM_HUMANPolymorphism1047891AT1406N
08UniProtVAR_064066P1411LCPSM_HUMANDisease (CPS1D)  ---AP1411L
09UniProtVAR_066140P1439LCPSM_HUMANDisease (CPS1D)  ---AP1439L
10UniProtVAR_066170T1443ACPSM_HUMANDisease (CPS1D)  ---AT1443A
11UniProtVAR_064067R1453QCPSM_HUMANDisease (CPS1D)  ---AR1453Q
12UniProtVAR_064068R1453WCPSM_HUMANDisease (CPS1D)  ---AR1453W
13UniProtVAR_066141P1462RCPSM_HUMANDisease (CPS1D)  ---AP1462R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (13, 26)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_066137R1371LCPSM_HUMANDisease (CPS1D)  ---AR1371L
02UniProtVAR_017568G1376SCPSM_HUMANPolymorphism140578009AG1376S
03UniProtVAR_066169A1378TCPSM_HUMANDisease (CPS1D)  ---AA1378T
04UniProtVAR_075413L1381SCPSM_HUMANDisease (CPS1D)  ---AL1381S
05UniProtVAR_066138T1391MCPSM_HUMANDisease (CPS1D)  ---AT1391M
06UniProtVAR_066139L1398VCPSM_HUMANDisease (CPS1D)  ---AL1398V
07UniProtVAR_017569T1406NCPSM_HUMANPolymorphism1047891AT1406N
08UniProtVAR_064066P1411LCPSM_HUMANDisease (CPS1D)  ---AP1411L
09UniProtVAR_066140P1439LCPSM_HUMANDisease (CPS1D)  ---AP1439L
10UniProtVAR_066170T1443ACPSM_HUMANDisease (CPS1D)  ---AT1443A
11UniProtVAR_064067R1453QCPSM_HUMANDisease (CPS1D)  ---AR1453Q
12UniProtVAR_064068R1453WCPSM_HUMANDisease (CPS1D)  ---AR1453W
13UniProtVAR_066141P1462RCPSM_HUMANDisease (CPS1D)  ---AP1462R

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YVQ)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  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:134
 aligned with CPSM_HUMAN | P31327 from UniProtKB/Swiss-Prot  Length:1500

    Alignment length:140
                                  1348      1358      1368      1378      1388      1398      1408      1418      1428      1438      1448      1458      1468      1478
          CPSM_HUMAN   1339 GEGIHTAFLKAMLSTGFKIPQKGILIGIQQSFRPRFLGVAEQLHNEGFKLFATEATSDWLNANNVPATPVAWPSQEGQNPSLSSIRKLIRDGSIDLVINLPNNNTKFVHDNYVIRRTAVDSGIPLLTNFQVTKLFAEAVQ 1478
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --- ------------------------------MGS-2yvqA01 A:1373-1465                                                                      ------------- Pfam domains
         Sec.struct. author ...-hhhhhhhhh.........eeeee.hhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhh....eee.hhhhh-----..hhhhhhhh....eeee....hhhhhhhhhhhhhhhhhh...ee.hhhhhhhhhhh.. Sec.struct. author
             SAPs(SNPs) (1) --------------------------------L----S-T--S---------M------V-------N----L---------------------------L---A---------Q--------R---------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------------------------------------W------------------------- SAPs(SNPs) (2)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2yvq A    5 SSG-HTAFLKAMLSTGFKIPQKGILIGIQQSFRPRFLGVAEQLHNEGFKLFATEATSDWLNANNVPATPVAWPSQE-----LSSIRKLIRDGSIDLVINLPNNNTKFVHDNYVIRRTAVDSGIPLLTNFQVTKLFAEAVQ 1478
                              | | 1348      1358      1368      1378      1388      1398      1408     |   - |    1428      1438      1448      1458      1468      1478
                              7 |                                                                   1414  1420                                                          
                             1343                                                                                                                                       

   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  (0, 0)

(no "SCOP Domain" information available for 2YVQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Family: MGS (13)

(-) Gene Ontology  (60, 60)

Asymmetric Unit(hide GO term definitions)
Chain A   (CPSM_HUMAN | P31327)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004070    aspartate carbamoyltransferase activity    Catalysis of the reaction: L-aspartate + carbamoyl phosphate = N-carbamoyl-L-aspartate + H(+) + phosphate.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0004087    carbamoyl-phosphate synthase (ammonia) activity    Catalysis of the reaction: 2 ATP + CO(2) + H(2)O + NH(4)(+) = 2 ADP + carbamoyl phosphate + 5 H(+) + phosphate.
    GO:0004088    carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity    Catalysis of the reaction: 2 ATP + L-glutamine + CO2 + H2O = 2 ADP + phosphate + glutamate + carbamoyl phosphate.
    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:0004151    dihydroorotase activity    Catalysis of the reaction: (S)-dihydroorotate + H(2)O = N-carbamoyl-L-aspartate + H(+).
    GO:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    GO:0016595    glutamate binding    Interacting selectively and non-covalently with glutamate, the anion of 2-aminopentanedioic acid.
    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:0072341    modified amino acid binding    Interacting selectively and non-covalently with a modified amino acid.
    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:0005543    phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
    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:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006207    'de novo' pyrimidine nucleobase biosynthetic process    The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
    GO:0055081    anion homeostasis    Any process involved in the maintenance of an internal steady state of anions within an organism or cell.
    GO:0006526    arginine biosynthetic process    The chemical reactions and pathways resulting in the formation of arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
    GO:0070409    carbamoyl phosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of carbamoyl phosphate, an intermediate in the urea cycle and other nitrogen compound metabolic pathways.
    GO:0071320    cellular response to cAMP    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
    GO:0044344    cellular response to fibroblast growth factor stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an fibroblast growth factor stimulus.
    GO:0071377    cellular response to glucagon stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucagon stimulus.
    GO:0071400    cellular response to oleic acid    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an oleic acid stimulus.
    GO:0019240    citrulline biosynthetic process    The chemical reactions and pathways resulting in the formation of citrulline, N5-carbamoyl-L-ornithine, an alpha amino acid not found in proteins.
    GO:0006541    glutamine metabolic process    The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid.
    GO:0005980    glycogen catabolic process    The chemical reactions and pathways resulting in the breakdown of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues.
    GO:0070365    hepatocyte differentiation    The process in which a relatively unspecialized cell acquires the specialized features of a hepatocyte. A hepatocyte is specialized epithelial cell that is organized into interconnected plates called lobules, and is the main structural component of the liver.
    GO:0050667    homocysteine metabolic process    The chemical reactions and pathways involving homocysteine, the amino acid alpha-amino-gamma-mercaptobutanoic acid. Homocysteine is an important intermediate in the metabolic reactions of its S-methyl derivative, methionine.
    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: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:0007494    midgut development    The process whose specific outcome is the progression of the midgut over time, from its formation to the mature structure. The midgut is the middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine.
    GO:0046209    nitric oxide metabolic process    The chemical reactions and pathways involving nitric oxide, nitrogen monoxide (NO), a colorless gas only slightly soluble in water.
    GO:0006807    nitrogen compound metabolic process    The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0014075    response to amine    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 amine stimulus. An amine is a compound formally derived from ammonia by replacing one, two or three hydrogen atoms by hydrocarbyl groups.
    GO:0043200    response to amino acid    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 amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups.
    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:0071548    response to dexamethasone    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 dexamethasone stimulus.
    GO:0042493    response to drug    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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0032094    response to food    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 food stimulus; food is anything which, when taken into the body, serves to nourish or build up the tissues or to supply body heat.
    GO:0033762    response to glucagon    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 glucagon 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.
    GO:0060416    response to growth hormone    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 growth hormone stimulus. Growth hormone is a peptide hormone that binds to the growth hormone receptor and stimulates growth.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0034201    response to oleic acid    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 oleic acid stimulus.
    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.
    GO:0048545    response to steroid hormone    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 steroid hormone stimulus.
    GO:0009636    response to toxic 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 a toxic stimulus.
    GO:0010043    response to zinc ion    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 zinc ion stimulus.
    GO:0019433    triglyceride catabolic process    The chemical reactions and pathways resulting in the breakdown of a triglyceride, any triester of glycerol.
    GO:0000050    urea cycle    The sequence of reactions by which arginine is synthesized from ornithine, then cleaved to yield urea and regenerate ornithine. The overall reaction equation is NH3 + CO2 + aspartate + 3 ATP + 2 H2O = urea + fumarate + 2 ADP + 2 phosphate + AMP + diphosphate.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    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:0042645    mitochondrial nucleoid    The region of a mitochondrion to which the DNA is confined.
    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:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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

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        CPSM_HUMAN | P313274utr 4utv 4utx 4utz 4uu7 4uu8 4uua 4uub 5dot 5dou

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