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(-) Description

Title :  CRYSTAL STRUCTURE OF PIKA GITRL
 
Authors :  P. R. Kumar, R. Bhosle, J. Bonanno, S. Chowdhury, A. Gizzi, S. Glen, B. Hi J. Hammonds, R. Seidel, R. Toro, S. G. Nathenson, S. C. Almo, New York Structural Genomics Research Consortium (Nysgrc), Atoms-To-A The Immune Function Network (Ifn)
Date :  13 Mar 12  (Deposition) - 21 Mar 12  (Release) - 21 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,F  (1x)
Biol. Unit 2:  C,D,E  (1x)
Keywords :  Gitrl, Glucocorticoid-Induced Tnf Receptor Ligand, Immune System, Tnfrsf18, Structural Genomics, Psi-Biology, New York Structural Genomics Research Consortium, Nysgrc, Ifn (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. R. Kumar, R. Bhosle, J. Bonanno, S. Chowdhury, A. Gizzi, S. Glen, B. Hillerich, J. Hammonds, R. Seidel, R. Toro, S. G. Nathenson, S. C. Almo
Crystal Structure Of Gitrl From Ochotona Princeps
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 18
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET28B WITH N-TERMINAL SMT3 TAG
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GITRL
    Organism Scientific: OCHOTONA PRINCEPS
    Organism Taxid: 9978
    Strain: SYNTHETIC GENE

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB   F
Biological Unit 2 (1x):   CDE 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
2MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:42 , GLU A:89 , LYS B:9 , TYR B:46 , PHE F:58BINDING SITE FOR RESIDUE GOL A 201
2AC2SOFTWAREARG B:36 , GLY B:93 , ASP B:94 , ASN C:40 , GLN C:122BINDING SITE FOR RESIDUE GOL B 201
3AC3SOFTWAREGLY C:47 , ARG C:48 , ILE C:81 , ASN C:83 , HOH C:340BINDING SITE FOR RESIDUE GOL C 201
4AC4SOFTWARESER C:31 , ASP C:32 , TRP C:33 , GLU C:97 , HOH C:314BINDING SITE FOR RESIDUE GOL C 202
5AC5SOFTWARELYS C:67 , TYR C:88 , GLU C:89 , HOH C:326 , ARG D:48 , ASN D:83 , TYR D:112BINDING SITE FOR RESIDUE GOL D 201
6AC6SOFTWAREASN E:52 , TYR E:55 , SER E:78BINDING SITE FOR RESIDUE GOL E 201
7AC7SOFTWARELYS E:3BINDING SITE FOR RESIDUE GOL E 202
8AC8SOFTWARELYS B:67 , TYR B:88 , GLU B:89 , GLY F:47 , ARG F:48 , ASN F:83 , TYR F:112 , HOH F:318BINDING SITE FOR RESIDUE GOL F 201
9AC9SOFTWAREASP B:104 , GLU F:16 , ASP F:32BINDING SITE FOR RESIDUE MG F 202

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:6 -A:26
2B:6 -B:26
3C:6 -C:26
4D:6 -D:26
5E:6 -E:26
6F:6 -F:26

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Gly A:11 -Pro A:12
2Ser A:13 -Pro A:14
3Gly B:11 -Pro B:12
4Ser B:13 -Pro B:14
5Gly C:11 -Pro C:12
6Ser C:13 -Pro C:14
7Gly D:11 -Pro D:12
8Ser D:13 -Pro D:14
9Gly E:11 -Pro E:12
10Ser E:13 -Pro E:14
11Gly F:11 -Pro F:12
12Ser F:13 -Pro F:14

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E4S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4E4S)

(-) Exons   (0, 0)

(no "Exon" information available for 4E4S)

(-) 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:113
                                                                                                                                                 
               SCOP domains d4e4sa_ A: Glucocorticoid-induced TNF-related ligand, TNFSF18                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee......eeee..eeeee..eeee...eeeeeeeee.............eeeee..eeeeee......ee..eeeee....eeeeee.hhhhhhhhhheeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 4e4s A   5 PCVAKFGPSPSEWQMASCLNKMSDWKLRILQNGLYAIYGRVTPNPTYKGFAPFEVQLCKNKDAIQTLTDSSKIQNLGNIYEFNAGDTIELRFNSDDQVLKTNTYFGIILLANP 121
                                    14     || 28        38        48        58        68        78        88        98       108       118   
                                          20|                                                                                                
                                           25                                                                                                


Chain B from PDB  Type:PROTEIN  Length:115
                                                                                                                                                   
               SCOP domains d4e4sb_ B: Glucocorticoid-induced TNF-related ligand, TNFSF18                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee......eeee.....eeeee..eeee...eeeeeeeee.............eeeee..eeeee......ee..eeeee....eeeeee.hhhhhhhhhheeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 4e4s B   5 PCVAKFGPSPSEWQMASSESCLNKMSDWKLRILQNGLYAIYGRVTPNPTYKGFAPFEVQLCKNDAIQTLTDSSKIQNLGNIYEFNAGDTIELRFNSDDQVLKTNTYFGIILLANP 121
                                    14        25        35        45        55        65  ||    76        86        96       106       116     
                                             23|                                         68|                                                   
                                              25                                          70                                                   


Chain C from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains d4e4sc_ C: Glucocorticoid-induced TNF-related ligand, TNFSF18                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee......eeee..eeeee..eeee...eeeeeeeee.............eeeee..eeeeee......ee..eeeee....eeeeee.hhhhhhhhhheeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4e4s C   5 PCVAKFGPSPSEWQMASCLNKMSDWKLRILQNGLYAIYGRVTPNPTYKGFAPFEVQLCKNKDAIQTLTDSSKIQNLGNIYEFNAGDTIELRFNSDDQVLKTNTYFGIILLANPQ 122
                                    14     || 28        38        48        58        68        78        88        98       108       118    
                                          20|                                                                                                 
                                           25                                                                                                 


Chain D from PDB  Type:PROTEIN  Length:112
                                                                                                                                                
               SCOP domains d4e4sd_ D: Glucocorticoid-induced TNF-related ligand, TNFSF18                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee......ee...eeeee..eeee...eeeeeeeee.............eeeee..eeeeee......ee..eeeee....eeeeee.hhhhhhhhhheeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 4e4s D   5 PCVAKFGPSPSEWQMSCLNKMSDWKLRILQNGLYAIYGRVTPNPTYKGFAPFEVQLCKNKDAIQTLTDSSKIQNLGNIYEFNAGDTIELRFNSDDQVLKTNTYFGIILLANP 121
                                    14    ||  29        39        49        59        69        79        89        99       109       119  
                                         19|                                                                                                
                                          25                                                                                                


Chain E from PDB  Type:PROTEIN  Length:119
                                                                                                                                                       
               SCOP domains d4e4se_ E: Glucocorticoid-induced TNF-related ligand, TNFSF18                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee......eee......eeeee..eeee...eeeeeeeee.............eeeee..eeeeee......ee..eeeee....eeeeee.hhhhh.....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 4e4s E   3 KDPCVAKFGPSPSEWQMASSESCLNKMSDWKLRILQNGLYAIYGRVTPNPTYKGFAPFEVQLCKNKDAIQTLTDSSKIQNLGNIYEFNAGDTIELRFNSDDQVLKTNTYFGIILLANPQ 122
                                    12        22||      33        43        53        63        73        83        93       103       113         
                                               23|                                                                                                 
                                                25                                                                                                 


Chain F from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains d4e4sf_ F: Glucocorticoid-induced TNF-related ligand, TNFSF18                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee......ee...eeeee..eeee...eeeeeeeee.............eeeee..eeeeee......ee..eeeee....eeeeee.hhhhhhhhhheeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4e4s F   5 PCVAKFGPSPSEWQMSCLNKMSDWKLRILQNGLYAIYGRVTPNPTYKGFAPFEVQLCKNKDAIQTLTDSSKIQNLGNIYEFNAGDTIELRFNSDDQVLKTNTYFGIILLANPQF 123
                                    14    ||  29        39        49        59        69        79        89        99       109       119    
                                         19|                                                                                                  
                                          25
   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, 6)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4E4S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E4S)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4E4S)

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