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(-) Description

Title :  CRYSTAL STRUCTURE OF THE EXOSITE-CONTAINING FRAGMENT OF HUMAN ADAMTS13 (P475S MUTANT)
 
Authors :  D. Nakayama, M. Akiyama, S. Takeda, K. Kokame, J. Takagi, T. Miyata
Date :  21 Dec 11  (Deposition) - 26 Dec 12  (Release) - 26 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Nakayama, M. Akiyama, S. Takeda, K. Kokame, J. Takagi, T. Miyata
Structural Analysis And Biochemical Studies Of Adamts13 P475S Mutant
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - A DISINTEGRIN AND METALLOPROTEINASE WITH THROMBOSPONDIN MOTIFS 13
    ChainsA
    EC Number3.4.24.87
    EngineeredYES
    Expression SystemCRICETULUS GRISEUS
    Expression System Cell LineHEK293S GNT1-
    Expression System CommonCHINESE HAMSTER
    Expression System PlasmidPCM-NIDSP
    Expression System Taxid10029
    Expression System Vector TypePLASMID
    FragmentDTCS DOMAINS, UNP RESIDUES 287-685
    GeneADAMTS13
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymADAM-TS 13, ADAM-TS13, ADAMTS-13, VON WILLEBRAND FACTOR- CLEAVING PROTEASE, VWF-CP, VWF-CLEAVING PROTEASE

 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  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2BMA1Ligand/IonBETA-D-MANNOSE
3FUC1Ligand/IonALPHA-L-FUCOSE
4NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (4, 6)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2BMA1Ligand/IonBETA-D-MANNOSE
3FUC1Ligand/IonALPHA-L-FUCOSE
4NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (4, 12)
No.NameCountTypeFull Name
1BGC2Ligand/IonBETA-D-GLUCOSE
2BMA2Ligand/IonBETA-D-MANNOSE
3FUC2Ligand/IonALPHA-L-FUCOSE
4NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:551 , ASN A:552BINDING SITE FOR RESIDUE NAG A 900
2AC2SOFTWAREARG A:386 , TRP A:387 , ARG A:409 , VAL A:424 , HOH A:1043BINDING SITE FOR RESIDUE BMA A 905
3AC3SOFTWAREASN A:614 , VAL A:630 , HOH A:1027BINDING SITE FOR LINKED RESIDUES A 901 to 902
4AC4SOFTWAREARG A:398 , SER A:399 , CYS A:400 , PHE A:445 , GLN A:448 , HOH A:1009 , HOH A:1032BINDING SITE FOR LINKED RESIDUES A 903 to 904

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:311 -A:337
2A:322 -A:347
3A:332 -A:366
4A:360 -A:371
5A:396 -A:433
6A:400 -A:438
7A:411 -A:423
8A:450 -A:487
9A:483 -A:522
10A:508 -A:527
11A:532 -A:548
12A:545 -A:555

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Thr A:378 -Pro A:379
2Asn A:413 -Pro A:414
3Tyr A:617 -Pro A:618

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (23, 23)

Asymmetric Unit (23, 23)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_067777Y304CATS13_HUMANDisease (TTP)281875285AY304C
02UniProtVAR_067778C311YATS13_HUMANDisease (TTP)281875336AC311Y
03UniProtVAR_067779T339RATS13_HUMANPolymorphism149517360AT339R
04UniProtVAR_067780C347SATS13_HUMANDisease (TTP)281875294AC347S
05UniProtVAR_067781R349CATS13_HUMANDisease (TTP)281875288AR349C
06UniProtVAR_067782P353LATS13_HUMANDisease (TTP)281875338AP353L
07UniProtVAR_027118W390CATS13_HUMANDisease (TTP)281875306AW390C
08UniProtVAR_027119R398HATS13_HUMANDisease (TTP)121908471AR398H
09UniProtVAR_027120Q448EATS13_HUMANPolymorphism2301612AQ448E
10UniProtVAR_027162Q456HATS13_HUMANPolymorphism36220239AQ456H
11UniProtVAR_027163P457LATS13_HUMANPolymorphism36220240AP457L
12UniProtVAR_027121P475SATS13_HUMANPolymorphism11575933AS475S
13UniProtVAR_067783R507QATS13_HUMANDisease (TTP)281875296AR507Q
14UniProtVAR_027122C508YATS13_HUMANDisease (TTP)281875305AC508Y
15UniProtVAR_067784G525DATS13_HUMANDisease (TTP)281875286AG525D
16UniProtVAR_027123R528GATS13_HUMANDisease (TTP)121908473AR528G
17UniProtVAR_067785A596VATS13_HUMANDisease (TTP)281875299AA596V
18UniProtVAR_067786A606PATS13_HUMANDisease (TTP)281875290AA606P
19UniProtVAR_027124P618AATS13_HUMANPolymorphism28647808AP618A
20UniProtVAR_027125R625HATS13_HUMANPolymorphism36090624AR625H
21UniProtVAR_067787Y658CATS13_HUMANDisease (TTP)281875335AY658C
22UniProtVAR_067788P671LATS13_HUMANDisease (TTP)281875295AP671L
23UniProtVAR_027126I673FATS13_HUMANDisease (TTP)281875307AI673F

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (23, 23)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_067777Y304CATS13_HUMANDisease (TTP)281875285AY304C
02UniProtVAR_067778C311YATS13_HUMANDisease (TTP)281875336AC311Y
03UniProtVAR_067779T339RATS13_HUMANPolymorphism149517360AT339R
04UniProtVAR_067780C347SATS13_HUMANDisease (TTP)281875294AC347S
05UniProtVAR_067781R349CATS13_HUMANDisease (TTP)281875288AR349C
06UniProtVAR_067782P353LATS13_HUMANDisease (TTP)281875338AP353L
07UniProtVAR_027118W390CATS13_HUMANDisease (TTP)281875306AW390C
08UniProtVAR_027119R398HATS13_HUMANDisease (TTP)121908471AR398H
09UniProtVAR_027120Q448EATS13_HUMANPolymorphism2301612AQ448E
10UniProtVAR_027162Q456HATS13_HUMANPolymorphism36220239AQ456H
11UniProtVAR_027163P457LATS13_HUMANPolymorphism36220240AP457L
12UniProtVAR_027121P475SATS13_HUMANPolymorphism11575933AS475S
13UniProtVAR_067783R507QATS13_HUMANDisease (TTP)281875296AR507Q
14UniProtVAR_027122C508YATS13_HUMANDisease (TTP)281875305AC508Y
15UniProtVAR_067784G525DATS13_HUMANDisease (TTP)281875286AG525D
16UniProtVAR_027123R528GATS13_HUMANDisease (TTP)121908473AR528G
17UniProtVAR_067785A596VATS13_HUMANDisease (TTP)281875299AA596V
18UniProtVAR_067786A606PATS13_HUMANDisease (TTP)281875290AA606P
19UniProtVAR_027124P618AATS13_HUMANPolymorphism28647808AP618A
20UniProtVAR_027125R625HATS13_HUMANPolymorphism36090624AR625H
21UniProtVAR_067787Y658CATS13_HUMANDisease (TTP)281875335AY658C
22UniProtVAR_067788P671LATS13_HUMANDisease (TTP)281875295AP671L
23UniProtVAR_027126I673FATS13_HUMANDisease (TTP)281875307AI673F

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (23, 46)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_067777Y304CATS13_HUMANDisease (TTP)281875285AY304C
02UniProtVAR_067778C311YATS13_HUMANDisease (TTP)281875336AC311Y
03UniProtVAR_067779T339RATS13_HUMANPolymorphism149517360AT339R
04UniProtVAR_067780C347SATS13_HUMANDisease (TTP)281875294AC347S
05UniProtVAR_067781R349CATS13_HUMANDisease (TTP)281875288AR349C
06UniProtVAR_067782P353LATS13_HUMANDisease (TTP)281875338AP353L
07UniProtVAR_027118W390CATS13_HUMANDisease (TTP)281875306AW390C
08UniProtVAR_027119R398HATS13_HUMANDisease (TTP)121908471AR398H
09UniProtVAR_027120Q448EATS13_HUMANPolymorphism2301612AQ448E
10UniProtVAR_027162Q456HATS13_HUMANPolymorphism36220239AQ456H
11UniProtVAR_027163P457LATS13_HUMANPolymorphism36220240AP457L
12UniProtVAR_027121P475SATS13_HUMANPolymorphism11575933AS475S
13UniProtVAR_067783R507QATS13_HUMANDisease (TTP)281875296AR507Q
14UniProtVAR_027122C508YATS13_HUMANDisease (TTP)281875305AC508Y
15UniProtVAR_067784G525DATS13_HUMANDisease (TTP)281875286AG525D
16UniProtVAR_027123R528GATS13_HUMANDisease (TTP)121908473AR528G
17UniProtVAR_067785A596VATS13_HUMANDisease (TTP)281875299AA596V
18UniProtVAR_067786A606PATS13_HUMANDisease (TTP)281875290AA606P
19UniProtVAR_027124P618AATS13_HUMANPolymorphism28647808AP618A
20UniProtVAR_027125R625HATS13_HUMANPolymorphism36090624AR625H
21UniProtVAR_067787Y658CATS13_HUMANDisease (TTP)281875335AY658C
22UniProtVAR_067788P671LATS13_HUMANDisease (TTP)281875295AP671L
23UniProtVAR_027126I673FATS13_HUMANDisease (TTP)281875307AI673F

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TSP1PS50092 Thrombospondin type-1 (TSP1) repeat profile.ATS13_HUMAN384-439
742-805
1072-1131
1012-1068
  1A:384-439
-
-
-
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TSP1PS50092 Thrombospondin type-1 (TSP1) repeat profile.ATS13_HUMAN384-439
742-805
1072-1131
1012-1068
  1A:384-439
-
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TSP1PS50092 Thrombospondin type-1 (TSP1) repeat profile.ATS13_HUMAN384-439
742-805
1072-1131
1012-1068
  2A:384-439
-
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 3VN4)

(-) 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:375
 aligned with ATS13_HUMAN | Q76LX8 from UniProtKB/Swiss-Prot  Length:1427

    Alignment length:385
                                   307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677     
          ATS13_HUMAN   298 DAQPGLYYSANEQCRVAFGPKAVACTFAREHLDMCQALSCHTDPLDQSSCSRLLVPLLDGTECGVEKWCSKGRCRSLVELTPIAAVHGRWSSWGPRSPCSRSCGGGVVTRRRQCNNPRPAFGGRACVGADLQAEMCNTQACEKTQLEFMSQQCARTDGQPLRSSPGGASFYHWGAAVPHSQGDALCRHMCRAIGESFIMKRGDSFLDGTRCMPSGPREDGTLSLCVSGSCRTFGCDGRMDSQQVWDRCQVCGGDNSTCSPRKGSFTAGRAREYVTFLTVTPNLTSVYIANHRPLFTHLAVRIGGRYVVAGKMSISPNTTYPSLLEDGRVEYRVALTEDRLPRLEEIRIWGPLQEDADIQVYRRYGEEYGNLTRPDITFTYFQPKP 682
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.hhhhhhhhhhh........---.......eee..........eee.............eeee..eeeehhhhh........................eeeeee...................eeeeee.......hhhhhhhhhhhh......-------....ee......hhhhhhh.eeee.....eee.....................eeeee..eeeee........................eeeeeeee.......eeeeeee....eeeeeee.....eeeeeee..eeee.........eee.......eeeeeeee.....eeeeeeeee......eeeeeee..hhhhhhhhh..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------C------Y---------------------------R-------S-C---L------------------------------------C-------H-------------------------------------------------E-------HL-----------------S-------------------------------QY----------------D--G-------------------------------------------------------------------V---------P-----------A------H--------------------------------C------------L-F--------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------TSP1  PDB: A:384-439 UniProt: 384-439                   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vn4 A 298 DAQPGLYYSANEQCRVAFGPKAVACTF---HLDMCQALSCHTDPLDQSSCSRLLVPLLDGTECGVEKWCSKGRCRSLVELTPIAAVHGRWSSWGPRSPCSRSCGGGVVTRRRQCNNPRPAFGGRACVGADLQAEMCNTQACEKTQLEFMSQQCARTDGQPL-------SFYHWGAAVSHSQGDALCRHMCRAIGESFIMKRGDSFLDGTRCMPSGPREDGTLSLCVSGSCRTFGCDGRMDSQQVWDRCQVCGGDNSTCSPRKGSFTAGRAREYVTFLTVTPNLTSVYIANHRPLFTHLAVRIGGRYVVAGKMSISPNTTYPSLLEDGRVEYRVALTEDRLPRLEEIRIWGPLQEDADIQVYRRYGEEYGNLTRPDITFTYFQPKP 682
                                   307       317      |  -|      337       347       357       367       377       387       397       407       417       427       437       447       457|      467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677     
                                                    324 328                                                                                                                               458     466                                                                                                                                                                                                                        

   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 3VN4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VN4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VN4)

(-) Gene Ontology  (29, 29)

Asymmetric Unit(hide GO term definitions)
Chain A   (ATS13_HUMAN | Q76LX8)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    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:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0007160    cell-matrix adhesion    The binding of a cell to the extracellular matrix via adhesion molecules.
    GO:0009100    glycoprotein metabolic process    The chemical reactions and pathways involving glycoproteins, any protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide.
    GO:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    GO:0007229    integrin-mediated signaling pathway    A series of molecular signals initiated by the binding of extracellular ligand to an integrin on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0043171    peptide catabolic process    The chemical reactions and pathways resulting in the breakdown of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.
    GO:0030168    platelet activation    A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
    GO:0036066    protein O-linked fucosylation    The process of transferring a fucosyl group to a serine or threonine residues in a protein acceptor molecule, to form an O-linked protein-sugar linkage.
    GO:0016485    protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0034341    response to interferon-gamma    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 interferon-gamma stimulus. Interferon-gamma is also known as type II interferon.
    GO:0070670    response to interleukin-4    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 interleukin-4 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:0034612    response to tumor necrosis factor    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 tumor necrosis factor stimulus.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005578    proteinaceous extracellular matrix    A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

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  ATS13_HUMAN | Q76LX8
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        ATS13_HUMAN | Q76LX83ghm 3ghn

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3ghm 3ghn