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(-) Description

Title :  STRUCTURE OF HUMAN NPC1 MIDDLE LUMENAL DOMAIN BOUND TO NPC2
 
Authors :  X. Li
Date :  19 Jul 16  (Deposition) - 24 Aug 16  (Release) - 14 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.41
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Human Protein Complex, Npc1, Npc2, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Li, P. Saha, J. Li, G. Blobel, S. R. Pfeffer
Clues To The Mechanism Of Cholesterol Transfer From The Structure Of Npc1 Middle Lumenal Domain Bound To Npc2.
Proc. Natl. Acad. Sci. Usa V. 113 10079 2016
PubMed-ID: 27551080  |  Reference-DOI: 10.1073/PNAS.1611956113

(-) Compounds

Molecule 1 - NIEMANN-PICK C1 PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: BACTERIA
    Expression System Cell Line: BL21(DE3)
    Expression System Taxid: 2
    Fragment: UNP RESIDUES 374-620
    Gene: NPC1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - EPIDIDYMAL SECRETORY PROTEIN E1
    Chains: C, D
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 20-151
    Gene: NPC2, HE1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HUMAN EPIDIDYMIS-SPECIFIC PROTEIN 1,HE1,NIEMANN-PICK DISEASE TYPE C2 PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1C3S2Ligand/IonCHOLEST-5-EN-3-YL HYDROGEN SULFATE
2NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE C:85 , VAL C:115 , TYR C:119binding site for residue C3S C 203
2AC2SOFTWARETYR D:55 , PHE D:85 , TYR D:119 , PRO D:120 , ILE D:122binding site for residue C3S D 203
3AC3SOFTWAREASN C:58 , THR C:60 , LEU C:110binding site for Mono-Saccharide NAG C 201 bound to ASN C 58
4AC4SOFTWAREVAL B:517 , ARG B:518 , PRO B:520 , TRP B:544 , GLN B:553 , TYR B:555 , GLN C:131 , ASN C:135 , HOH C:314binding site for Mono-Saccharide NAG C 202 bound to ASN C 135
5AC5SOFTWAREASN D:58 , THR D:60 , SER D:108 , LEU D:110binding site for Mono-Saccharide NAG D 201 bound to ASN D 58
6AC6SOFTWAREVAL A:517 , ARG A:518 , TRP A:544 , GLN A:553 , TYR A:555 , GLN D:129 , GLN D:131 , ASN D:135binding site for Mono-Saccharide NAG D 202 bound to ASN D 135

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:468 -A:479
2A:516 -A:533
3B:468 -B:479
4B:516 -B:533
5C:27 -C:140
6C:42 -C:47
7C:93 -C:99
8D:27 -D:140
9D:42 -D:47
10D:93 -D:99

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1Tyr A:423 -Pro A:424
2Ser A:473 -Pro A:474
3Tyr B:423 -Pro B:424
4Ser B:473 -Pro B:474
5Ser C:40 -Pro C:41
6Gln C:45 -Pro C:46
7Cys C:99 -Pro C:100
8Ser D:40 -Pro D:41
9Gln D:45 -Pro D:46
10Cys D:99 -Pro D:100

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KWY)

(-) Sequences/Alignments

Asymmetric/Biological 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:208
                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee......eee........eeehhhhhhhhhhhhhhhhhhhhh.eeee..eeee.hhh...............hhhhhhh.hhhhhhh.ee....eeehhhhhhhhhh........................hhhh.ee.....hhhhh.eeeeeeeee....hhhhhhhhhhhhhhhhhhhhh......eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kwy A 400 GPFFRTEQLIIRAPLTDKHIYQPYPSGADVPFGPPLDIQILHQVLDLQIAIENITASYDNETVTLQDICLAPLSPYNTNCTILSVLNYFQNSHSVLDHKKGDDFFVYADYHTHFLYCVRAPASLNDTSLLHDPCLGTFGGPVFPWLVLGGYDDQNYNNATALVITFPVNNYYNDTEKLQRAQAWEKEFINFVKNYKNPNLTISFTAER 607
                                   409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599        


Chain B from PDB  Type:PROTEIN  Length:236
                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.....eeeeeeee......eee........eeehhhhhhhhhhhhhhhhhhhhh.eeee..eeeehhhhh..............hhhhhhh.hhhhhh..ee....eeehhhhhhhhhh........................hhhh.ee.....hhhhh.eeeeeeee.....hhhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kwy B 378 VDLWSAPSSQARLEKEYFDQHFGPFFRTEQLIIRAPLTDKHIYQPYPSGADVPFGPPLDIQILHQVLDLQIAIENITASYDNETVTLQDICLAPLSPYNTNCTILSVLNYFQNSHSVLDHKKGDDFFVYADYHTHFLYCVRAPASLNDTSLLHDPCLGTFGGPVFPWLVLGGYDDQNYNNATALVITFPVNNYYNDTEKLQRAQAWEKEFINFVKNYKNPNLTISFTAERSIEDEL 613
                                   387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607      


Chain C from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.....eeeeeeeee......eeee..eeeeeeeeeee.......eeeeeeee..eeee......hhhhh.........eeeeeeeeeee.......eeeeeeeee.....eeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kwy C  20 EPVQFKDCGSVDGVIKEVNVSPCPTQPCQLSKGQSYSVNVTFTSNIQSKSSKAVVHGILMGVPVPFPIPEPDGCKSGINCPIQKDKTYSYLNKLPVKSEYPSIKLVVEWQLQDDKNQSLFCWEIPVQIVSHLA 152
                                    29        39        49        59        69        79        89        99       109       119       129       139       149   


Chain D from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....ee.....eeeeeeeee......eeee..eeeeeeeeeee.......eeeeeeee..eeeee.....hhhhh..........eeeeeeeeee.......eeeeeeeee.....eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5kwy D  20 EPVQFKDCGSVDGVIKEVNVSPCPTQPCQLSKGQSYSVNVTFTSNIQSKSSKAVVHGILMGVPVPFPIPEPDGCKSGINCPIQKDKTYSYLNKLPVKSEYPSIKLVVEWQLQDDKNQSLFCWEIPVQIVSHL 151
                                    29        39        49        59        69        79        89        99       109       119       129       139       149
   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 5KWY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (54, 66)

Asymmetric/Biological Unit(hide GO term definitions)

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  NPC2_HUMAN | P61916
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 Related Entries

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

UniProtKB/Swiss-Prot
        NPC1_HUMAN | O15118: 3gkh 3gki 3gkj 3jd8 5f18 5f1b 5hns 5i31 5jnx

(-) Related Entries Specified in the PDB File

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