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(-) Description

Title :  TRANSGLUTAMINASE 2 UNDERGOES LARGE CONFORMATIONAL CHANGE UPON ACTIVATION
 
Authors :  P. Strop, D. M. Pinkas, A. T. Brunger, C. Khosla
Date :  30 May 07  (Deposition) - 23 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,X
Biol. Unit 1:  A,X  (1x)
Biol. Unit 2:  A,X  (2x)
Keywords :  Transglutaminase 2, Tissue Transglutaminase, Tg2, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. M. Pinkas, P. Strop, A. T. Brunger, C. Khosla
Transglutaminase 2 Undergoes A Large Conformational Change Upon Activation
Plos Biol. V. 5 E327 2007
PubMed-ID: 18092889  |  Reference-DOI: 10.1371/JOURNAL.PBIO.0050327

(-) Compounds

Molecule 1 - TRANSGLUTAMINASE 2
    ChainsA
    EC Number2.3.2.13
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneTGM2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTISSUE TRANSGLUTAMINASE, TGASE C, TGC, TGC, TRANSGLUTAMINASE-2, TGASE- H
 
Molecule 2 - POLYPEPTIDE
    ChainsX
    EngineeredYES
    Other DetailsCHEMICALLY SYNTHESIZED.
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AX
Biological Unit 1 (1x)AX
Biological Unit 2 (2x)AX

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2NH21Mod. Amino AcidAMINO GROUP
3ONL1Mod. Amino Acid5-OXO-L-NORLEUCINE
4SO45Ligand/IonSULFATE ION
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2NH21Mod. Amino AcidAMINO GROUP
3ONL1Mod. Amino Acid5-OXO-L-NORLEUCINE
4SO45Ligand/IonSULFATE ION
Biological Unit 2 (4, 16)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2NH22Mod. Amino AcidAMINO GROUP
3ONL2Mod. Amino Acid5-OXO-L-NORLEUCINE
4SO410Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:202 , ARG A:222 , GLY A:367 , THR A:368BINDING SITE FOR RESIDUE SO4 A 688
2AC2SOFTWARELYS A:202 , ARG A:209 , TYR A:219 , HOH A:728 , HOH A:931 , HOH A:947BINDING SITE FOR RESIDUE SO4 A 689
3AC3SOFTWAREARG A:80BINDING SITE FOR RESIDUE SO4 A 690
4AC4SOFTWAREARG A:80 , ASP A:81 , ALA A:82 , HOH A:753 , HOH A:873BINDING SITE FOR RESIDUE SO4 A 691
5AC5SOFTWAREARG A:478 , VAL A:479 , GLY A:480 , ARG A:580BINDING SITE FOR RESIDUE SO4 A 692

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:370 -A:371

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys A:273 -Tyr A:274
2Cys A:370 -Cys A:371
3Gly A:372 -Pro A:373
4Lys A:387 -Tyr A:388

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (7, 7)

Asymmetric Unit (7, 7)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_052553R76HTGM2_HUMANPolymorphism41274720AR76H
2UniProtVAR_055357R214HTGM2_HUMANPolymorphism45530133AR214H
3UniProtVAR_037998M330RTGM2_HUMANUnclassified141603506AM330R
4UniProtVAR_037999I331NTGM2_HUMANUnclassified  ---AI331N
5UniProtVAR_055359R436WTGM2_HUMANPolymorphism45629036AR436W
6UniProtVAR_052554P536STGM2_HUMANPolymorphism45556333AP536S
7UniProtVAR_036554G660VTGM2_HUMANUnclassified  ---AG660V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (7, 7)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_052553R76HTGM2_HUMANPolymorphism41274720AR76H
2UniProtVAR_055357R214HTGM2_HUMANPolymorphism45530133AR214H
3UniProtVAR_037998M330RTGM2_HUMANUnclassified141603506AM330R
4UniProtVAR_037999I331NTGM2_HUMANUnclassified  ---AI331N
5UniProtVAR_055359R436WTGM2_HUMANPolymorphism45629036AR436W
6UniProtVAR_052554P536STGM2_HUMANPolymorphism45556333AP536S
7UniProtVAR_036554G660VTGM2_HUMANUnclassified  ---AG660V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (7, 14)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_052553R76HTGM2_HUMANPolymorphism41274720AR76H
2UniProtVAR_055357R214HTGM2_HUMANPolymorphism45530133AR214H
3UniProtVAR_037998M330RTGM2_HUMANUnclassified141603506AM330R
4UniProtVAR_037999I331NTGM2_HUMANUnclassified  ---AI331N
5UniProtVAR_055359R436WTGM2_HUMANPolymorphism45629036AR436W
6UniProtVAR_052554P536STGM2_HUMANPolymorphism45556333AP536S
7UniProtVAR_036554G660VTGM2_HUMANUnclassified  ---AG660V

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRANSGLUTAMINASESPS00547 Transglutaminases active site.TGM2_HUMAN275-292  1A:275-292
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRANSGLUTAMINASESPS00547 Transglutaminases active site.TGM2_HUMAN275-292  1A:275-292
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRANSGLUTAMINASESPS00547 Transglutaminases active site.TGM2_HUMAN275-292  2A:275-292

(-) Exons   (13, 13)

Asymmetric Unit (13, 13)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003614752aENSE00001922845chr20:36793774-36793591184TGM2_HUMAN1-441A:1-44
1.3bENST000003614753bENSE00000800527chr20:36790001-36789822180TGM2_HUMAN4-64611A:4-6461
1.4aENST000003614754aENSE00000661931chr20:36784491-36784249243TGM2_HUMAN64-145821A:64-14582
1.5bENST000003614755bENSE00000661930chr20:36779459-36779341119TGM2_HUMAN145-184401A:145-18440
1.6ENST000003614756ENSE00000800526chr20:36776491-36776363129TGM2_HUMAN185-227431A:185-22743
1.7bENST000003614757bENSE00000800525chr20:36775296-36775119178TGM2_HUMAN228-287601A:228-28760
1.8ENST000003614758ENSE00000661927chr20:36770601-36770466136TGM2_HUMAN287-332461A:287-332 (gaps)46
1.9ENST000003614759ENSE00000661926chr20:36769787-36769684104TGM2_HUMAN332-367361A:332-36736
1.10ENST0000036147510ENSE00000661925chr20:36768056-36767814243TGM2_HUMAN367-448821A:367-448 (gaps)82
1.11aENST0000036147511aENSE00000661924chr20:36766787-36766515273TGM2_HUMAN448-539921A:448-539 (gaps)92
1.12bENST0000036147512bENSE00000661923chr20:36760902-36760742161TGM2_HUMAN539-592541A:539-59254
1.13bENST0000036147513bENSE00000661922chr20:36759631-36759495137TGM2_HUMAN593-638461A:593-63846
1.14aENST0000036147514aENSE00001904837chr20:36758771-367568631909TGM2_HUMAN638-687501A:638-68346

(-) 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:655
 aligned with TGM2_HUMAN | P21980 from UniProtKB/Swiss-Prot  Length:687

    Alignment length:683
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680   
           TGM2_HUMAN     1 MAEELVLERCDLELETNGRDHHTADLCREKLVVRRGQPFWLTLHFEGRNYEASVDSLTFSVVTGPAPSQEAGTKARFPLRDAVEEGDWTATVVDQQDCTLSLQLTTPANAPIGLYRLSLEASTGYQGSSFVLGHFILLFNAWCPADAVYLDSEEERQEYVLTQQGFIYQGSAKFIKNIPWNFGQFEDGILDICLILLDVNPKFLKNAGRDCSRRSSPVYVGRVVSGMVNCNDDQGVLLGRWDNNYGDGVSPMSWIGSVDILRRWKNHGCQRVKYGQCWVFAAVACTVLRCLGIPTRVVTNYNSAHDQNSNLLIEYFRNEFGEIQGDKSEMIWNFHCWVESWMTRPDLQPGYEGWQALDPTPQEKSEGTYCCGPVPVRAIKEGDLSTKYDAPFVFAEVNADVVDWIQQDDGSVHKSINRSLIVGLKISTKSVGRDEREDITHTYKYPEGSSEEREAFTRANHLNKLAEKEETGMAMRIRVGQSMNMGSDFDVFAHITNNTAEEYVCRLLLCARTVSYNGILGPECGTKYLLNLNLEPFSEKSVPLCILYEKYRDCLTESNLIKVRALLVEPVINSYLLAERDLYLENPEIKIRILGEPKQKRKLVAEVSLQNPLPVALEGCTFTVEGAGLTEEQKTVEIPDPVEAGEEVKVRMDLLPLHMGLHKLVVNFESDKLKAVKGFRNVI 683
               SCOP domains --------------d2q3za1 A:15-145 Transglutaminase N-terminal domain                                                                                d2q3za4 A:146-461 Transglutaminase catalytic domain                                                                                                                                                                                                                                                                                   d2q3za2 A:472-585 Transglutaminase, two C-terminal domains                                                        d2q3za3 A:586-683 Transglutaminase, two C-terminal domains                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----Transglut_N-2q3zA04 A:5-124                                                                                             -----------------------------------------------------------------------------------------------------------------------------------Transglut_core-2q3zA03 A:256-359                                                                        -----------------------------------------------       ------------------------------------------------          -------------------------------------------------------------------------------------------------------------------Transglut_C-2q3zA01 A:587-683                                                                     Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Transglut_C-2q3zA02 A:587-683                                                                     Pfam domains (2)
         Sec.struct. author ......eeeee.hhhhhhhhh.hhhhh....eee....eeeeeee.........eeeeeeeee..........eeeee..........eeeeeee...eeeeeee.......eeeeeeeeeee..eeeeeeeeeeeee.............hhhhhhhhh...eeeeeee....eeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.........eee.................hhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhh..eeeeeeeeee..--.hhhhhhhhh---------......eeeeeeeee..........eeeee................eehhhhhh.......hhhhhhhhhh.eeeee..-------.ee...eeeeeeeeee......eeehhhhhh....hhhhhhhhhhhhh----------.eeeeee..........eeeeeeeee.....eeeeeeeeeeee.....eeeeeeeeeeeeeee...eeeeeeeeehhhhhh.......eeeeeeeeee....eeeeeeeeee......eeeee........eeeeeeee.........eeeeee........eeeee........eeeeeeee.......eeeeeeee......eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------H-----------------------------------------------------------------------------------------------------------------------------------------H-------------------------------------------------------------------------------------------------------------------RN--------------------------------------------------------------------------------------------------------W---------------------------------------------------------------------------------------------------S---------------------------------------------------------------------------------------------------------------------------V----------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRANSGLUTAMINASES ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.2a-----------------------------------------------------------Exon 1.4a  PDB: A:64-145 UniProt: 64-145                                          ---------------------------------------Exon 1.6  PDB: A:185-227 UniProt: 185-227  Exon 1.7b  PDB: A:228-287 UniProt: 228-287                  -------------------------------------------------------------------------------Exon 1.10  PDB: A:367-448 (gaps) UniProt: 367-448                                 ------------------------------------------------------------------------------------------Exon 1.12b  PDB: A:539-592 UniProt: 539-592           Exon 1.13b  PDB: A:593-638 UniProt: 593-638   --------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.3b  PDB: A:4-64 UniProt: 4-64                         --------------------------------------------------------------------------------Exon 1.5b  PDB: A:145-184               ------------------------------------------------------------------------------------------------------Exon 1.8  PDB: A:287-332 (gaps)               -------------------------------------------------------------------------------------------------------------------Exon 1.11a  PDB: A:448-539 (gaps) UniProt: 448-539                                          --------------------------------------------------------------------------------------------------Exon 1.14a  PDB: A:638-683 UniProt: 638-687    Transcript 1 (2)
           Transcript 1 (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: A:332-367            ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (3)
                 2q3z A   1 MAEELVLERCDLELETNGRDHHTADLCREKLVVRRGQPFWLTLHFEGRNYQASVDSLTFSVVTGPAPSQEAGTKARFPLRDAVEEGDWTATVVDQQDCTLSLQLTTPANAPIGLYRLSLEASTGYQGSSFVLGHFILLFNAWCPADAVYLDSEEERQEYVLTQQGFIYQGSAKFIKNIPWNFGQFQDGILDICLILLDVNPKFLKNAGRDCSRRSSPVYVGRVGSGMVNCNDDQGVLLGRWDNNYGDGVSPMSWIGSVDILRRWKNHGCQRVKYGQCWVFAAVACTVLRCLGIPTRVVTNYNSAHD--SNLLIEYFRN---------SEMIWNFHCWVESWMTRPDLQPGYEGWQALDPTPQEKSEGTYCCGPVPVRAIKEGDLSTKYDAPFVFAEVNADVVDWIQ-------KSINRSLIVGLKISTKSVGRDEREDITHTYKYPEGSSEEREAFTRANH----------GMAMRIRVGQSMNMGSDFDVFAHITNNTAEEYVCRLLLCARTVSYNGILGPECGTKYLLNLTLEPFSEKSVPLCILYEKYRDCLTESNLIKVRALLVEPVINSYLLAERDLYLENPEIKIRILGEPKQKRKLVAEVSLQNPLPVALEGCTFTVEGAGLTEEQKTVEIPDPVEAGEEVKVRMDLVPLHMGLHKLVVNFESDKLKAVKGFRNVI 683
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300     | 310       | -       330       340       350       360       370       380       390       400     |   -   |   420       430       440       450       460|        - |     480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680   
                                                                                                                                                                                                                                                                                                                                           306  |      318       328                                                                           406     414                                            461        472                                                                                                                                                                                                                   
                                                                                                                                                                                                                                                                                                                                              309                                                                                                                                                                                                                                                                                                                                                                                      

Chain X from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 2q3z X   1 xPxLPFx   7
                            | |   |
                            1-ACE |
                              3-ONL
                                  7-NH2

   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  (3, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Q3Z)

(-) Pfam Domains  (3, 4)

Asymmetric Unit
(-)
Clan: E-set (290)

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A   (TGM2_HUMAN | P21980)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0003810    protein-glutamine gamma-glutamyltransferase activity    Catalysis of the reaction: protein glutamine + alkylamine = protein N5-alkylglutamine + NH3. This reaction is the formation of the N6-(L-isoglutamyl)-L-lysine isopeptide, resulting in cross-linking polypeptide chains; the gamma-carboxamide groups of peptidyl-glutamine residues act as acyl donors, and the 6-amino-groups of peptidyl-lysine residues act as acceptors, to give intra- and intermolecular N6-(5-glutamyl)lysine cross-links.
    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.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
    GO:0043277    apoptotic cell clearance    The recognition and removal of an apoptotic cell by a neighboring cell or by a phagocyte.
    GO:0060445    branching involved in salivary gland morphogenesis    The process in which the branching structure of the salivary gland is generated and organized.
    GO:0032471    negative regulation of endoplasmic reticulum calcium ion concentration    Any process that decreases the concentration of calcium ions in the endoplasmic reticulum.
    GO:0018149    peptide cross-linking    The formation of a covalent cross-link between or within protein chains.
    GO:0007200    phospholipase C-activating G-protein coupled receptor signaling pathway    The series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand, where the pathway proceeds with activation of phospholipase C (PLC) and a subsequent increase in the concentration of inositol trisphosphate (IP3) and diacylglycerol (DAG).
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0045785    positive regulation of cell adhesion    Any process that activates or increases the frequency, rate or extent of cell adhesion.
    GO:0051561    positive regulation of mitochondrial calcium ion concentration    Any process that increases the concentration of calcium ions in mitochondria.
    GO:0060662    salivary gland cavitation    The process in which the solid core of salivary epithelium gives rise to the hollow tube of the gland.
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:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0031226    intrinsic component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane.
    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.

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  TGM2_HUMAN | P21980
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TGM2_HUMAN | P219801fau 1kv3 3ly6 3s3j 3s3p 3s3s 4pyg

(-) Related Entries Specified in the PDB File

1kv3