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(-) Description

Title :  CRYSTAL STRUCTURE OF MONOMER HUMAN CELLULAR RETINOL BINDING PROTEIN II-Y60L
 
Authors :  Z. Assar, Z. Nossoni, W. Wang, J. H. Gieger, B. Borhan
Date :  27 Aug 15  (Deposition) - 21 Sep 16  (Release) - 21 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
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 :  Domain Swapping, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Assar, Z. Nossoni, W. Wang, J. H. Geiger, B. Borhan
Crystal Structure Of Monomer Human Cellular Retinol Binding Protein Ii-Y60L
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RETINOL-BINDING PROTEIN 2
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET17B
    Expression System Strain: BL21-DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RBP2, CRBP2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CELLULAR RETINOL-BINDING PROTEIN II,CRBP-II

 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  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:72 , GLN A:97 , TRP A:106 , HOH A:318 , HOH A:340binding site for residue ACT A 201
2AC2SOFTWARELYS A:40 , GLN A:108binding site for residue ACT A 202
3AC3SOFTWARELYS D:40 , TRP D:106 , GLN D:108binding site for residue ACT D 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DG4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DG4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DG4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DG4)

(-) Exons   (0, 0)

(no "Exon" information available for 5DG4)

(-) 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:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeehhhhhhhhh..hhhhhhhhh....eeeeeee..eeeeeee....eeeeeee....eeee.......eeeeeeeee..eeeeeee......eeeeeee..eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dg4 A   1 TRDQNGTWEMESNENFEGYMKALDIDFATRKIAVRLTQTKVIDQDGDNFKTKTTSTFRNLDVDFTVGVEFDEYTKSLDNRHVKALVTWEGDVLVCVQKGEKENRGWKQWIEGDKLYLELTCGDQVCRQVFKKK 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   


Chain B from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeehhhhhhhhh..hhhhhhhhh....eeeeeee..eeeeeee....eeeeeee....eeee.......eeeeeeeee..eeeeeee......eeeeeee..eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dg4 B   1 TRDQNGTWEMESNENFEGYMKALDIDFATRKIAVRLTQTKVIDQDGDNFKTKTTSTFRNLDVDFTVGVEFDEYTKSLDNRHVKALVTWEGDVLVCVQKGEKENRGWKQWIEGDKLYLELTCGDQVCRQVFKKK 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   


Chain C from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeehhhhhhhhh..hhhhhhhhh....eeeeeee..eeeeeee....eeeeeee....eeee.......eeeeeeeee..eeeeeee......eeeeeee..eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dg4 C   1 TRDQNGTWEMESNENFEGYMKALDIDFATRKIAVRLTQTKVIDQDGDNFKTKTTSTFRNLDVDFTVGVEFDEYTKSLDNRHVKALVTWEGDVLVCVQKGEKENRGWKQWIEGDKLYLELTCGDQVCRQVFKKK 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   


Chain D from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeehhhhhhhhh..hhhhhhhhh....eeeeeee..eeeeeee....eeeeeee....eeee.......eeeeeeeee..eeeeeee......eeeeeee..eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dg4 D   1 TRDQNGTWEMESNENFEGYMKALDIDFATRKIAVRLTQTKVIDQDGDNFKTKTTSTFRNLDVDFTVGVEFDEYTKSLDNRHVKALVTWEGDVLVCVQKGEKENRGWKQWIEGDKLYLELTCGDQVCRQVFKKK 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   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 5DG4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DG4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DG4)

(-) Gene Ontology  (11, 11)

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 Related Entries

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UniProtKB/Swiss-Prot
        RET2_HUMAN | P50120: 2rcq 2rct 4ede 4eej 4efg 4exz 4gkc 4qyn 4qyp 4qzt 4qzu 4ruu 4zcb 4zgu 4zh6 4zh9 4zj0 4zr2 5dpq 5f58 5f6b 5f7g 5faz 5fen 5ffh

(-) Related Entries Specified in the PDB File

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