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(-) Description

Title :  THE CRYSTAL STRUCTURE OF REM1 IN COMPLEX WITH GDP
 
Authors :  A. P. Turnbull, E. Papagrigoriou, E. Ugochukwu, J. M. Elkins, M. Sounda X. Yang, F. Gorrec, C. Umeano, E. Salah, N. Burgess, C. Johansson, G. Be O. Gileadi, J. Bray, B. Marsden, S. Watts, F. Von Delft, J. Weigelt, A. C. H. Arrowsmith, M. Sundstrom, D. Doyle, Structural Genomics Cons (Sgc)
Date :  23 Nov 06  (Deposition) - 12 Dec 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A (1x),C (1x)
Keywords :  Rem1, Gdp/Gtp Binding, Gtp Hydrolysis, Rad And Gem Like Gtp Binding Protein 1, Structural Genomics, Structural Genomics Consortium, Sgc, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. P. Turnbull, E. Papagrigoriou, E. Ugochukwu, J. M. Elkins, M. Soundararajan, X. Yang, F. Gorrec, C. Umeano, E. Salah, N. Burgess, C. Johansson, G. Berridge, O. Gileadi, J. Bray, B. Marsden, S. Watts, F. Von Delft, J. Weigelt, A. Edwards, C. H. Arrowsmith, M. Sundstrom, D. Doyle
The Crystal Structure Of Rem1 In Complex With Gdp
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GTP-BINDING PROTEIN REM 1
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)-R3/ROSETTA
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneREM1, GES, REM
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRAD AND GEM-LIKE GTP-BINDING PROTEIN 1, GTPASE-REGULATING ENDOTHELIAL CELL SPROUTING

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D
Biological Unit 5 (1x)A (1x) C (1x) 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GDP4Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 5 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:1 , HOH A:2 , HOH A:3 , HOH A:4 , THR A:94 , GDP A:1001BINDING SITE FOR RESIDUE MG A 252
02AC2SOFTWAREHOH B:5 , HOH B:6 , HOH B:7 , HOH B:8 , THR B:94 , GDP B:1002BINDING SITE FOR RESIDUE MG B 252
03AC3SOFTWAREHOH C:9 , HOH C:10 , HOH C:11 , HOH C:12 , THR C:94 , GDP C:1003BINDING SITE FOR RESIDUE MG C 252
04AC4SOFTWAREHOH D:13 , HOH D:14 , HOH D:15 , HOH D:16 , THR D:94 , GDP D:1004BINDING SITE FOR RESIDUE MG D 252
05AC5SOFTWARESER B:162 , LYS B:196BINDING SITE FOR RESIDUE CL B 253
06AC6SOFTWARESER A:162 , LYS A:196BINDING SITE FOR RESIDUE CL A 253
07AC7SOFTWAREHOH A:2 , HOH A:3 , HOH A:4 , GLY A:90 , VAL A:91 , GLY A:92 , LYS A:93 , THR A:94 , SER A:95 , ASN A:195 , LYS A:196 , ASP A:198 , LEU A:199 , SER A:225 , ALA A:226 , THR A:227 , MG A:252BINDING SITE FOR RESIDUE GDP A 1001
08AC8SOFTWAREHOH B:5 , HOH B:6 , HOH B:7 , PRO B:89 , GLY B:90 , VAL B:91 , GLY B:92 , LYS B:93 , THR B:94 , SER B:95 , ASN B:195 , LYS B:196 , ASP B:198 , SER B:225 , ALA B:226 , THR B:227 , MG B:252BINDING SITE FOR RESIDUE GDP B 1002
09AC9SOFTWAREHOH C:9 , HOH C:10 , HOH C:12 , PRO C:89 , GLY C:90 , VAL C:91 , GLY C:92 , LYS C:93 , THR C:94 , SER C:95 , ASN C:195 , LYS C:196 , ASP C:198 , LEU C:199 , SER C:225 , ALA C:226 , THR C:227 , MG C:252BINDING SITE FOR RESIDUE GDP C 1003
10BC1SOFTWAREHOH D:13 , HOH D:15 , HOH D:16 , PRO D:89 , GLY D:90 , VAL D:91 , GLY D:92 , LYS D:93 , THR D:94 , SER D:95 , ASN D:195 , LYS D:196 , ASP D:198 , SER D:225 , ALA D:226 , THR D:227 , MG D:252BINDING SITE FOR RESIDUE GDP D 1004

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2NZJ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (4, 16)

Asymmetric Unit (4, 16)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002019791ENSE00001018615chr20:30063096-3006316974REM1_HUMAN-00--
1.2ENST000002019792ENSE00000859838chr20:30064030-30064588559REM1_HUMAN1-1141144A:0-114 (gaps)
B:0-114
C:0-114 (gaps)
D:0-114 (gaps)
37
37
37
37
1.3ENST000002019793ENSE00000661077chr20:30065631-3006571383REM1_HUMAN114-141284A:114-136
B:114-137
C:114-137
D:114-137
23
24
24
24
1.4ENST000002019794ENSE00000661078chr20:30070090-30070291202REM1_HUMAN142-209684A:144-209 (gaps)
B:144-209 (gaps)
C:144-209
D:144-209
66
66
66
66
1.5ENST000002019795ENSE00001018614chr20:30071962-30072708747REM1_HUMAN209-298904A:209-248
B:209-248
C:209-247
D:209-246
40
40
39
38

(-) 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:155
 aligned with REM1_HUMAN | O75628 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:171
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247 
           REM1_HUMAN    78 EALYRVVLLGDPGVGKTSLASLFAGKQERDLHEQLGEDVYERTLTVDGEDTTLVVVDTWEAEKLDKSWSQESCLQGGSAYVIVYSIADRGSFESASELRIQLRRTHQADHVPIILVGNKADLARCREVSVEEGRACAVVFDCKFIETSATLQHNVAELFEGVVRQLRLRRR 248
               SCOP domains d2nzja_ A: automated match     es                                                                                                                                           SCOP domains
               CATH domains 2nzjA00 A:0-248 P-loop con     taining nucleotide triphosph       ate hydrolases                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhh.-----.......eeeeeeee..eeeeeeee...-------hhhhhhh.....eeeeeee..hhhhhhhhhhhhhhhhhh----...eeeeee..........hhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:0-114 (gaps)        ---------------------------Exon 1.4  PDB: A:144-209 (gaps) UniProt: 142-209 [INCOMPLETE]       --------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.3  PDB: A:114-136    -------------------------------------------------------------------Exon 1.5  PDB: A:209-248 [INCOMPLETE]    Transcript 1 (2)
                 2nzj A   0 MALYRVVLLGDPGVGKTSLASLFAGK-----HEQLGEDVYERTLTVDGEDTTLVVVDTW-------SWSQESCLQGGSAYVIVYSIADRGSFESASELRIQLRRT----HVPIILVGNKADLARCREVSVEEGRACAVVFDCKFIETSATLQHNVAELFEGVVRQLRLRRR 248
                            ||      87        97     |   - |     117       127        |-      |147       157       167       177    |  187       197       207       217       227       237       247 
                            ||                     103   109                        136     144                                   182  187                                                             
                            0|                                                                                                                                                                         
                            79                                                                                                                                                                         

Chain B from PDB  Type:PROTEIN  Length:160
 aligned with REM1_HUMAN | O75628 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:171
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247 
           REM1_HUMAN    78 EALYRVVLLGDPGVGKTSLASLFAGKQERDLHEQLGEDVYERTLTVDGEDTTLVVVDTWEAEKLDKSWSQESCLQGGSAYVIVYSIADRGSFESASELRIQLRRTHQADHVPIILVGNKADLARCREVSVEEGRACAVVFDCKFIETSATLQHNVAELFEGVVRQLRLRRR 248
               SCOP domains d2nzjb_ B: automated matches                                                                                                                                                SCOP domains
               CATH domains 2nzjB00 B:0-248 P-loop containing nucleotide triphosphate hy      drolases                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhh.............eeeeeeee..eeeeeeee....------hhhhhhh.....eeeeeee..hhhhhhhhhhhhhhhhhh-----..eeeeee...hhhhh..hhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:0-114 UniProt: 1-114---------------------------Exon 1.4  PDB: B:144-209 (gaps) UniProt: 142-209 [INCOMPLETE]       --------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.3  PDB: B:114-137    -------------------------------------------------------------------Exon 1.5  PDB: B:209-248 [INCOMPLETE]    Transcript 1 (2)
                 2nzj B   0 MALYRVVLLGDPGVGKTSLASLFAGKQERDLHEQLGEDVYERTLTVDGEDTTLVVVDTWE------SWSQESCLQGGSAYVIVYSIADRGSFESASELRIQLRRT-----VPIILVGNKADLARCREVSVEEGRACAVVFDCKFIETSATLQHNVAELFEGVVRQLRLRRR 248
                            ||      87        97       107       117       127       137      |147       157       167       177    |    -|      197       207       217       227       237       247 
                            0|                                                       137    144                                   182   188                                                            
                            79                                                                                                                                                                         

Chain C from PDB  Type:PROTEIN  Length:159
 aligned with REM1_HUMAN | O75628 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:170
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247
           REM1_HUMAN    78 EALYRVVLLGDPGVGKTSLASLFAGKQERDLHEQLGEDVYERTLTVDGEDTTLVVVDTWEAEKLDKSWSQESCLQGGSAYVIVYSIADRGSFESASELRIQLRRTHQADHVPIILVGNKADLARCREVSVEEGRACAVVFDCKFIETSATLQHNVAELFEGVVRQLRLRR 247
               SCOP domains d2nzjc_ C: automated match     es                                                                                                                                          SCOP domains
               CATH domains 2nzjC00 C:0-247 P-loop con     taining nucleotide triphospha      te hydrolases                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhh.-----.......eeeeeeee..eeeeeeee....------hhhhhh......eeeeeee..hhhhhhhhhhhhhhhhh........eeeeee...hhhhh..hhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: C:0-114 (gaps)        ---------------------------Exon 1.4  PDB: C:144-209 UniProt: 142-209 [INCOMPLETE]              -------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.3  PDB: C:114-137    -------------------------------------------------------------------Exon 1.5  PDB: C:209-247 [INCOMPLETE]   Transcript 1 (2)
                 2nzj C   0 MALYRVVLLGDPGVGKTSLASLFAGK-----HEQLGEDVYERTLTVDGEDTTLVVVDTWE------SWSQESCLQGGSAYVIVYSIADRGSFESASELRIQLRRTHQADHVPIILVGNKADLARCREVSVEEGRACAVVFDCKFIETSATLQHNVAELFEGVVRQLRLRR 247
                            ||      87        97     |   - |     117       127       137      |147       157       167       177       187       197       207       217       227       237       247
                            0|                     103   109                         137    144                                                                                                       
                            79                                                                                                                                                                        

Chain D from PDB  Type:PROTEIN  Length:155
 aligned with REM1_HUMAN | O75628 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:169
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237         
           REM1_HUMAN    78 EALYRVVLLGDPGVGKTSLASLFAGKQERDLHEQLGEDVYERTLTVDGEDTTLVVVDTWEAEKLDKSWSQESCLQGGSAYVIVYSIADRGSFESASELRIQLRRTHQADHVPIILVGNKADLARCREVSVEEGRACAVVFDCKFIETSATLQHNVAELFEGVVRQLRLR 246
               SCOP domains d2nzjd_ D: automated matc        hes                                                                                                                                      SCOP domains
               CATH domains 2nzjD00 D:0-246 P-loop co        ntaining nucleotide triphos      phate hydrolases                                                                                        CATH domains
           Pfam domains (1) ----Ras-2nzjD01 D:82-245                                                                                                                                                - Pfam domains (1)
           Pfam domains (2) ----Ras-2nzjD02 D:82-245                                                                                                                                                - Pfam domains (2)
           Pfam domains (3) ----Ras-2nzjD03 D:82-245                                                                                                                                                - Pfam domains (3)
           Pfam domains (4) ----Ras-2nzjD04 D:82-245                                                                                                                                                - Pfam domains (4)
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhh--------.....eeeeeeee..eeeeeeee....------hhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhh........eeeeee...hhhhh..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: D:0-114 (gaps)        ---------------------------Exon 1.4  PDB: D:144-209 UniProt: 142-209 [INCOMPLETE]              ------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.3  PDB: D:114-137    -------------------------------------------------------------------Exon 1.5  PDB: D:209-246 [INCOMPLETE]  Transcript 1 (2)
                 2nzj D   0 MALYRVVLLGDPGVGKTSLASLFAG--------QLGEDVYERTLTVDGEDTTLVVVDTWE------SWSQESCLQGGSAYVIVYSIADRGSFESASELRIQLRRTHQADHVPIILVGNKADLARCREVSVEEGRACAVVFDCKFIETSATLQHNVAELFEGVVRQLRLR 246
                            ||      87        97    |    -   |   117       127       137      |147       157       167       177       187       197       207       217       227       237         
                            0|                    102      111                       137    144                                                                                                      
                            79                                                                                                                                                                       

   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, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Family: Ras (176)
1aRas-2nzjD01D:82-245
1bRas-2nzjD02D:82-245
1cRas-2nzjD03D:82-245
1dRas-2nzjD04D:82-245

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (REM1_HUMAN | O75628)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0005516    calmodulin binding    Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
    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.
biological process
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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