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(-) Description

Title :  STRUCTURE OF GLYCOSYLATED NPC1 LUMINAL DOMAIN C
 
Authors :  Y. Zhao, J. Ren, K. Harlos, D. I. Stuart
Date :  18 Jan 16  (Deposition) - 10 Feb 16  (Release) - 16 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Niemann-Pick Disease Type C, Npc1, Npc2, Cholesterol Transport, Ebola Virus Receptor, Ebola Virus Susceptibility, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zhao, J. Ren, K. Harlos, D. I. Stuart
Structure Of Glycosylated Npc1 Luminal Domain C Reveals Insights Into Npc2 And Ebola Virus Interactions.
Febs Lett. V. 590 605 2016
PubMed-ID: 26846330  |  Reference-DOI: 10.1002/1873-3468.12089

(-) Compounds

Molecule 1 - NIEMANN-PICK C1 PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293S
    Expression System Common: HUMAN
    Expression System Organ: KIDNEY
    Expression System Taxid: 9606
    Fragment: DOMAIN C, UNP RESIDUES 387-618
    Gene: NPC1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 27)

Asymmetric Unit (4, 27)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2MAN3Ligand/IonALPHA-D-MANNOSE
3NAG17Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SCN4Ligand/IonTHIOCYANATE ION
Biological Unit 1 (4, 13)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2MAN1Ligand/IonALPHA-D-MANNOSE
3NAG9Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SCN2Ligand/IonTHIOCYANATE ION
Biological Unit 2 (4, 14)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2MAN2Ligand/IonALPHA-D-MANNOSE
3NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SCN2Ligand/IonTHIOCYANATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:468 , ALA A:470 , SER A:473 , PRO A:474binding site for residue SCN A 712
02AC2SOFTWARETYR A:550binding site for residue SCN A 713
03AC3SOFTWAREGLU B:391 , GLY B:549binding site for residue SCN B 713
04AC4SOFTWAREGLN B:465 , ASP B:466 , CYS B:468 , TYR B:475 , ASN B:568binding site for residue SCN B 714
05AC5SOFTWARELEU A:472 , ASN A:476 , ASN A:478 , THR A:536binding site for Poly-Saccharide residues NAG A 710 through NAG A 711 bound to ASN A 478
06AC6SOFTWARELEU A:472 , ASN A:476 , ASN A:478 , THR A:536 , NAG A:711binding site for Mono-Saccharide NAG A 710 bound to ASN A 478
07AC7SOFTWAREASN A:524 , HIS A:530binding site for Poly-Saccharide residues NAG A 701 through NAG A 702 bound to ASN A 524
08AC8SOFTWAREALA A:427 , ASP A:428 , ASP A:551 , ASN A:554 , ASN A:556 , ASN A:557binding site for Poly-Saccharide residues NAG A 703 through MAN A 706 bound to ASN A 557
09AC9SOFTWARETYR A:571 , ASN A:572 , ASP A:573 , ASP B:552 , GLN B:553binding site for Mono-Saccharide NAG A 707 bound to ASN A 572
10AD1SOFTWAREGLN A:438 , GLN A:442 , ASN A:596 , ASN A:598 , BMA B:712binding site for Poly-Saccharide residues NAG A 708 through NAG A 709 bound to ASN A 598
11AD2SOFTWARELEU B:472 , ASN B:476 , ASN B:478 , THR B:536 , HOH B:807binding site for Poly-Saccharide residues NAG B 701 through NAG B 702 bound to ASN B 478
12AD3SOFTWARELEU B:472 , ASN B:476 , ASN B:478 , THR B:536 , NAG B:702 , HOH B:807binding site for Mono-Saccharide NAG B 701 bound to ASN B 478
13AD4SOFTWAREASN B:524binding site for Poly-Saccharide residues NAG B 703 through NAG B 704 bound to ASN B 524
14AD5SOFTWAREALA B:427 , ASP B:428 , PRO B:430 , ASN B:554 , ASN B:556 , ASN B:557 , HOH B:802binding site for Poly-Saccharide residues NAG B 705 through MAN B 709 bound to ASN B 557
15AD6SOFTWARENAG A:709 , GLN B:438 , GLN B:442 , ASN B:598binding site for Poly-Saccharide residues NAG B 710 through BMA B 712 bound to ASN B 598

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:468 -A:479
2A:516 -A:533
3B:468 -B:479
4B:516 -B:533

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:423 -Pro A:424
2Tyr B:423 -Pro B:424

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HNS)

(-) 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:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeeee......eee........eeehhhhhhhhhhhhhhhhhhhhh.eeee..eeeehhhhh..............hhhhhhh.hhhhhhh.ee....eeehhhhhhhhhh........................hhhhhee.....hhhhh.eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh.....eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hns A 392 KEYFDQHFGPFFRTEQLIIRAPLTDKHIYQPYPSGADVPFGPPLDIQILHQVLDLQIAIENITASYDNETVTLQDICLAPLSPYNTNCTILSVLNYFQNSHSVLDHKKGDDFFVYADYHTHFLYCVRAPASLNDTSLLHDPCLGTFGGPVFPWLVLGGYDDQNYNNATALVITFPVNNYYNDTEKLQRAQAWEKEFINFVKNYKNPNLTISFTAE 606
                                   401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601     


Chain B from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhh...eeeeeeeee......eee........eeehhhhhhhhhhhhhhhhhhhhh.eeee..eeeehhhhh..............hhhhhhh.hhhhhhh.ee....eeehhhhhhhhhh........................hhhhhee.....hhhhh.eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh.....eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5hns B 391 EKEYFDQHFGPFFRTEQLIIRAPLTDKHIYQPYPSGADVPFGPPLDIQILHQVLDLQIAIENITASYDNETVTLQDICLAPLSPYNTNCTILSVLNYFQNSHSVLDHKKGDDFFVYADYHTHFLYCVRAPASLNDTSLLHDPCLGTFGGPVFPWLVLGGYDDQNYNNATALVITFPVNNYYNDTEKLQRAQAWEKEFINFVKNYKNPNLTISFTAE 606
                                   400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 5HNS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (47, 47)

Asymmetric Unit(hide GO term definitions)

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        NPC1_HUMAN | O15118: 3gkh 3gki 3gkj 3jd8 5f18 5f1b 5i31 5jnx 5kwy

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