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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE MD-1 IN COMPLEX WITH PHOSPHATIDYLCHOLINE
 
Authors :  H. Harada, U. Ohto, Y. Satow
Date :  17 Mar 10  (Deposition) - 09 Jun 10  (Release) - 22 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
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)
Keywords :  Beta Sheet, Glycoprotein, Immunity, Inflammatory Response, Innate Immunity, Secreted, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Harada, U. Ohto, Y. Satow
Crystal Structure Of Mouse Md-1 With Endogenous Phospholipi Bound In Its Cavity
J. Mol. Biol. V. 400 838 2010
PubMed-ID: 20595044  |  Reference-DOI: 10.1016/J.JMB.2010.05.063

(-) Compounds

Molecule 1 - LYMPHOCYTE ANTIGEN 86
    Chains: A, B, C, D
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Gene: LY86, MD1
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: LY-86, PROTEIN MD-1

 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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 26)

Asymmetric Unit (4, 26)
No.NameCountTypeFull Name
1BEN16Ligand/IonBENZAMIDINE
2L9R2Ligand/Ion(2S)-3-(OCTADECANOYLOXY)-2-[(9Z)-OCTADEC-9-ENOYLOXY]PROPYL 2-(TRIMETHYLAMMONIO)ETHYL PHOSPHATE
3NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1BEN5Ligand/IonBENZAMIDINE
2L9R1Ligand/Ion(2S)-3-(OCTADECANOYLOXY)-2-[(9Z)-OCTADEC-9-ENOYLOXY]PROPYL 2-(TRIMETHYLAMMONIO)ETHYL PHOSPHATE
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NDG-1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1BEN3Ligand/IonBENZAMIDINE
2L9R-1Ligand/Ion(2S)-3-(OCTADECANOYLOXY)-2-[(9Z)-OCTADEC-9-ENOYLOXY]PROPYL 2-(TRIMETHYLAMMONIO)ETHYL PHOSPHATE
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
Biological Unit 3 (2, 5)
No.NameCountTypeFull Name
1BEN3Ligand/IonBENZAMIDINE
2L9R-1Ligand/Ion(2S)-3-(OCTADECANOYLOXY)-2-[(9Z)-OCTADEC-9-ENOYLOXY]PROPYL 2-(TRIMETHYLAMMONIO)ETHYL PHOSPHATE
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NDG-1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
Biological Unit 4 (3, 8)
No.NameCountTypeFull Name
1BEN5Ligand/IonBENZAMIDINE
2L9R1Ligand/Ion(2S)-3-(OCTADECANOYLOXY)-2-[(9Z)-OCTADEC-9-ENOYLOXY]PROPYL 2-(TRIMETHYLAMMONIO)ETHYL PHOSPHATE
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NDG-1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:41 , GLN A:43 , ASN A:156 , ALA A:157 , THR A:158 , HOH A:176BINDING SITE FOR RESIDUE NAG A 201
02AC2SOFTWARESER A:93 , ASN A:96 , HOH A:187 , HOH A:216 , HOH A:225 , HOH A:227 , HOH A:237 , HOH A:240 , HOH A:293 , ASN B:96 , CYS D:45 , PRO D:47BINDING SITE FOR RESIDUE NAG A 202
03AC3SOFTWAREILE A:55 , ILE A:62 , LEU A:87 , TYR A:97 , TYR A:122 , VAL A:126 , ASN A:127 , LEU A:142 , ALA A:153BINDING SITE FOR RESIDUE L9R A 301
04AC4SOFTWAREASP A:84 , ILE A:85 , THR A:86 , ASN A:96 , TYR A:97 , SER A:98 , BEN A:164 , NAG B:202 , HOH B:206 , HOH B:255 , ARG D:149 , THR D:151BINDING SITE FOR RESIDUE BEN A 163
05AC5SOFTWAREASP A:84 , GLU A:143 , BEN A:163 , BEN A:165 , HOH A:179 , GLU D:143 , TYR D:145 , ARG D:149BINDING SITE FOR RESIDUE BEN A 164
06AC6SOFTWAREGLU A:143 , TYR A:145 , ARG A:149 , BEN A:164 , HOH A:223 , ASP D:84 , GLU D:143 , TYR D:145 , BEN D:163BINDING SITE FOR RESIDUE BEN A 165
07AC7SOFTWAREPHE A:82 , GLU A:147 , ARG A:149 , HOH A:341 , GLU D:147 , ARG D:149BINDING SITE FOR RESIDUE BEN A 166
08AC8SOFTWAREGLY A:52 , LEU A:53 , SER A:54 , ARG A:69 , GLY A:71 , TYR A:121 , HOH A:178 , ARG B:114BINDING SITE FOR RESIDUE BEN A 167
09AC9SOFTWAREGLN B:139 , ASN B:156 , HOH B:188BINDING SITE FOR RESIDUE NDG B 201
10BC1SOFTWAREASN A:96 , SER A:98 , BEN A:163 , SER B:93 , ILE B:94 , ASN B:96 , BEN B:164 , HOH B:198 , HOH B:206 , HOH B:255 , ASP D:46 , LEU D:48 , GLN D:76 , ALA D:150 , THR D:151BINDING SITE FOR RESIDUE NAG B 202
11BC2SOFTWAREPHE B:82 , SER B:98 , TYR B:145 , GLU B:147 , HOH B:389 , PRO D:47BINDING SITE FOR RESIDUE BEN B 163
12BC3SOFTWAREHOH A:227 , ASP B:84 , THR B:86 , SER B:93 , ASN B:96 , LEU B:141 , GLU B:143 , ARG B:149 , NAG B:202 , LEU D:48BINDING SITE FOR RESIDUE BEN B 164
13BC4SOFTWAREGLY B:52 , GLY B:71 , ILE B:72 , ILE B:73 , GLN B:119 , HOH B:321BINDING SITE FOR RESIDUE BEN B 165
14BC5SOFTWAREASN C:156BINDING SITE FOR RESIDUE NAG C 201
15BC6SOFTWAREASP A:46 , LEU A:48 , GLN A:76 , ALA A:150 , THR A:151 , HOH A:241 , SER C:93 , ILE C:94 , ASN C:96 , BEN C:165 , HOH C:194 , HOH C:197 , ASN D:96 , SER D:98 , BEN D:163BINDING SITE FOR RESIDUE NAG C 202
16BC7SOFTWAREPRO A:47 , PHE C:82 , SER C:98 , TYR C:145 , GLU C:147 , HOH C:169 , HOH C:176BINDING SITE FOR RESIDUE BEN C 163
17BC8SOFTWAREPHE C:51 , GLY C:52 , GLY C:71 , ILE C:72 , HOH C:204 , ARG D:114 , HOH D:186BINDING SITE FOR RESIDUE BEN C 164
18BC9SOFTWAREASP C:84 , THR C:86 , MET C:88 , ASN C:96 , GLU C:143 , ARG C:149 , NAG C:202 , HOH D:220BINDING SITE FOR RESIDUE BEN C 165
19CC1SOFTWARELYS D:29 , VAL D:41 , GLN D:43 , ASN D:156 , ALA D:157 , THR D:158 , HOH D:192BINDING SITE FOR RESIDUE NAG D 201
20CC2SOFTWARECYS A:45 , PRO A:47 , ASN C:96 , SER D:93 , ILE D:94 , ASN D:96 , HOH D:185 , HOH D:212 , HOH D:220 , HOH D:221 , HOH D:225 , HOH D:231 , HOH D:233BINDING SITE FOR RESIDUE NAG D 202
21CC3SOFTWARETYR C:97 , ILE D:62 , LEU D:87 , TYR D:97 , TYR D:122 , ASN D:127 , PRO D:129 , TYR D:138BINDING SITE FOR RESIDUE L9R D 301
22CC4SOFTWAREARG A:149 , THR A:151 , BEN A:165 , HOH C:197 , NAG C:202 , ASP D:84 , ILE D:85 , THR D:86 , ASN D:96 , TYR D:97 , SER D:98BINDING SITE FOR RESIDUE BEN D 163
23CC5SOFTWAREHIS B:30 , HIS D:30 , THR D:31 , HOH D:334BINDING SITE FOR RESIDUE BEN D 164
24CC6SOFTWAREGLN C:61 , ILE C:62 , LEU C:131 , GLN D:61 , ILE D:62 , GLN D:63 , GLY D:130 , LEU D:131 , ASP D:132BINDING SITE FOR RESIDUE BEN D 165
25CC7SOFTWAREMET D:88 , HOH D:173 , HOH D:192BINDING SITE FOR RESIDUE BEN D 166
26CC8SOFTWAREGLY D:52 , ARG D:69BINDING SITE FOR RESIDUE BEN D 167

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:33 -A:58
2A:45 -A:154
3A:102 -A:112
4B:33 -B:58
5B:45 -B:154
6B:102 -B:112
7C:33 -C:58
8C:45 -C:154
9C:102 -C:112
10D:33 -D:58
11D:45 -D:154
12D:102 -D:112

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gln A:106 -Pro A:107

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M7O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3M7O)

(-) Exons   (0, 0)

(no "Exon" information available for 3M7O)

(-) 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:137
 aligned with LY86_MOUSE | O88188 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:137
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       
           LY86_MOUSE    26 GWPKHTACNSGGLEVVYQSCDPLQDFGLSIDQCSKQIQSNLNIRFGIILRQDIRKLFLDITLMAKGSSILNYSYPLCEEDQPKFSFCGRRKGEQIYYAGPVNNPGLDVPQGEYQLLLELYNENRATVACANATVTSS 162
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..eeeeeee.......eeee.....ee....eeeeeee......eeeeeeeeee..eeeeeeeeeeee...............eeeeeee....eee...eeeeeeeeeee....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m7o A  26 GWPKHTACNSGGLEVVYQSCDPLQDFGLSIDQCSKQIQSNLNIRFGIILRQDIRKLFLDITLMAKGSSILNYSYPLCEEDQPKFSFCGRRKGEQIYYAGPVNNPGLDVPQGEYQLLLELYNENRATVACANATVTSS 162
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       


Chain B from PDB  Type:PROTEIN  Length:131
 aligned with LY86_MOUSE | O88188 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:137
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       
           LY86_MOUSE    26 GWPKHTACNSGGLEVVYQSCDPLQDFGLSIDQCSKQIQSNLNIRFGIILRQDIRKLFLDITLMAKGSSILNYSYPLCEEDQPKFSFCGRRKGEQIYYAGPVNNPGLDVPQGEYQLLLELYNENRATVACANATVTSS 162
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..eeeeeee.......eeee.....ee....eeeeeee........eeeeeeee..eeeeeeeee..------..........eeeeeee.....ee...eeeeeeeeee.....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m7o B  26 GWPKHTACNSGGLEVVYQSCDPLQDFGLSIDQCSKQIQSNLNIRFGIILRQDIRKLFLDITLMAKGSSILNYSYPLC------FSFCGRRKGEQIYYAGPVNNPGLDVPQGEYQLLLELYNENRATVACANATVTSS 162
                                    35        45        55        65        75        85        95      |  -   |   115       125       135       145       155       
                                                                                                      102    109                                                     


Chain C from PDB  Type:PROTEIN  Length:131
 aligned with LY86_MOUSE | O88188 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:137
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       
           LY86_MOUSE    26 GWPKHTACNSGGLEVVYQSCDPLQDFGLSIDQCSKQIQSNLNIRFGIILRQDIRKLFLDITLMAKGSSILNYSYPLCEEDQPKFSFCGRRKGEQIYYAGPVNNPGLDVPQGEYQLLLELYNENRATVACANATVTSS 162
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..eeeeeee.......eeee.....ee....eeeeeee.......eeeeeeeee..eeeeeeeee..------..........eeeeeee.....ee...eeeeeeeeeee....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m7o C  26 GWPKHTACNSGGLEVVYQSCDPLQDFGLSIDQCSKQIQSNLNIRFGIILRQDIRKLFLDITLMAKGSSILNYSYPLC------FSFCGRRKGEQIYYAGPVNNPGLDVPQGEYQLLLELYNENRATVACANATVTSS 162
                                    35        45        55        65        75        85        95      |  -   |   115       125       135       145       155       
                                                                                                      102    109                                                     


Chain D from PDB  Type:PROTEIN  Length:131
 aligned with LY86_MOUSE | O88188 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:137
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       
           LY86_MOUSE    26 GWPKHTACNSGGLEVVYQSCDPLQDFGLSIDQCSKQIQSNLNIRFGIILRQDIRKLFLDITLMAKGSSILNYSYPLCEEDQPKFSFCGRRKGEQIYYAGPVNNPGLDVPQGEYQLLLELYNENRATVACANATVTSS 162
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------E1_DerP2_DerF2-3m7oD01 D:38-161                                                                                             - Pfam domains (1)
           Pfam domains (2) ------------E1_DerP2_DerF2-3m7oD02 D:38-161                                                                                             - Pfam domains (2)
           Pfam domains (3) ------------E1_DerP2_DerF2-3m7oD03 D:38-161                                                                                             - Pfam domains (3)
           Pfam domains (4) ------------E1_DerP2_DerF2-3m7oD04 D:38-161                                                                                             - Pfam domains (4)
         Sec.struct. author ....eeeeee..eeeeeee.......eeee.....ee....eeeeeee.......eeeeeeeee..eeeeeeeeeee------..........eeeeeee....eee...eeeeeeeeeee....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m7o D  26 GWPKHTACNSGGLEVVYQSCDPLQDFGLSIDQCSKQIQSNLNIRFGIILRQDIRKLFLDITLMAKGSSILNYSYPLC------FSFCGRRKGEQIYYAGPVNNPGLDVPQGEYQLLLELYNENRATVACANATVTSS 162
                                    35        45        55        65        75        85        95      |  -   |   115       125       135       145       155       
                                                                                                      102    109
   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 3M7O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M7O)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: E1_DerP2_DerF2] (8)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (LY86_MOUSE | O88188)
biological process
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0031666    positive regulation of lipopolysaccharide-mediated signaling pathway    Any process that activates or increases the frequency, rate or extent of signaling in response to detection of lipopolysaccharide.
cellular component
    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.

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  3m7o
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  LY86_MOUSE | O88188
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    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        LY86_MOUSE | O88188: 3t6q

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3M7O)