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(-) Description

Title :  MHC COMPLEXED TO 11MER PEPTIDE
 
Authors :  J. Liu, Y. Chai, J. Qi, G. F. Gao
Date :  30 Nov 15  (Deposition) - 30 Nov 16  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Mhc, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Xiao, W. Xiang, Y. Chai, J. Haywood, J. Qi, L. Ba, P. Qi, M. Wang, J. Liu G. F. Gao
Diversified Anchoring Features The Peptide Presentation Of Dla-88*50801: First Structural Insight Into Domestic Dog Mh Class I
J Immunol. V. 197 2306 2016
PubMed-ID: 27511732  |  Reference-DOI: 10.4049/JIMMUNOL.1600887

(-) Compounds

Molecule 1 - MHC CLASS I ANTIGEN
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DLA-88
    Organism Common: DOG
    Organism Scientific: CANIS LUPUS FAMILIARIS
    Organism Taxid: 9615
    Synonym: DLA-88*50801
 
Molecule 2 - BETA-2-MICROGLOBULIN
    Chains: B, E
    Engineered: YES
    Expression System: ESCHERICHIA
    Expression System Taxid: 561
    Expression System Vector Type: PLASMID
    Gene: B2M
    Organism Common: DOG
    Organism Scientific: CANIS LUPUS FAMILIARIS
    Organism Taxid: 9615
 
Molecule 3 - PEPTIDE FROM CYTOCHROME P450 FAMILY 1 SUBFAMILY B POLYPEPTIDE 1
    Chains: C, F
    Engineered: YES
    Organism Common: DOG
    Organism Scientific: CANIS LUPUS FAMILIARIS
    Organism Taxid: 9615
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5F1N)

(-) Sites  (0, 0)

(no "Site" information available for 5F1N)

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:101 -A:165
2A:204 -A:260
3B:52 -B:106
4D:101 -D:165
5D:204 -D:260
6E:52 -E:106

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Gly A:104 -Pro A:105
2Tyr A:210 -Pro A:211
3His B:58 -Pro B:59
4Tyr D:210 -Pro D:211
5His E:58 -Pro E:59

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F1N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F1N)

(-) Exons   (0, 0)

(no "Exon" information available for 5F1N)

(-) 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:275
                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee........eeeeeeee..eeeeeee........ee.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeee.....eeeeeeeeee..eeeeee......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee....eeeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeee..hhh.eeeeee.......eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f1n A   1 GSHSLRYFYTSVSRPGRGDPRFIAVGYVDDTQFVRFDSDAATGRTEPRAPWVEQEGPEYWDGETRKVKETAQVYRVDLDTLRGYYNQSEAGSHTIQTMYGCDLGPGGRLLRGYRQDAYDGADYIALNEDLRSWTAADTAAQITRRKWEAAGVAELQWRNYLETTCVEWLQRYLEMGKETLLRAEPPSTRVTRHPISDHEVTLRCWALGFYPAEITLTWQRDGEDQTQDTEVVDTRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLVEPVTRRW 275
                                    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     


Chain B from PDB  Type:PROTEIN  Length:99
                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.........eeeeeeeeee.....eeeeee..ee...ee...ee.....eeeeeeeee.......eeeeee.......eeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 5f1n B  27 AVQHPPKIQVYSRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMKAEQTDLSFSKDWTFYLLVHTEFTPNEQDEFSCRVKHVTLSEPQIVKWDRDN 125
                                    36        46        56        66        76        86        96       106       116         


Chain C from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ...hhhhh... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 5f1n C   1 RFLDKDGFIDK  11
                                    10 


Chain D from PDB  Type:PROTEIN  Length:275
                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee........eeeeeeee..eeeeeee........ee.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeee.hhh.eeeeeeeeee..eeeeee......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee....eeeeeeeeeee.....eeeeee..ee.....ee...ee.....eeeeeeeeee..hhh.eeeeee.......eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f1n D   1 GSHSLRYFYTSVSRPGRGDPRFIAVGYVDDTQFVRFDSDAATGRTEPRAPWVEQEGPEYWDGETRKVKETAQVYRVDLDTLRGYYNQSEAGSHTIQTMYGCDLGPGGRLLRGYRQDAYDGADYIALNEDLRSWTAADTAAQITRRKWEAAGVAELQWRNYLETTCVEWLQRYLEMGKETLLRAEPPSTRVTRHPISDHEVTLRCWALGFYPAEITLTWQRDGEDQTQDTEVVDTRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLVEPVTRRW 275
                                    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     


Chain E from PDB  Type:PROTEIN  Length:99
                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.........eeeeeeeeee.....eeeeee..ee...ee...ee.....eeeeeeeee.......eeeeee.......eeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 5f1n E  27 AVQHPPKIQVYSRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMKAEQTDLSFSKDWTFYLLVHTEFTPNEQDEFSCRVKHVTLSEPQIVKWDRDN 125
                                    36        46        56        66        76        86        96       106       116         


Chain F from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ...hhhhh... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 5f1n F   1 RFLDKDGFIDK  11
                                    10
   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 5F1N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F1N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F1N)

(-) Gene Ontology  (49, 52)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:104 - Pro A:105   [ RasMol ]  
    His B:58 - Pro B:59   [ RasMol ]  
    His E:58 - Pro E:59   [ RasMol ]  
    Tyr A:210 - Pro A:211   [ RasMol ]  
    Tyr D:210 - Pro D:211   [ RasMol ]  
 
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 Related Entries

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(-) Related Entries Specified in the PDB File

5f1i