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(-) Description

Title :  CRYSTAL STRUCTURE OF RETINOL-BINDING PROTEIN 4 (RBP4) IN COMPLEX WITH A NON-RETINOID LIGAND
 
Authors :  Z. Wang, S. Johnstone, N. Walker
Date :  07 Mar 14  (Deposition) - 02 Jul 14  (Release) - 02 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  B  (1x)
Biol. Unit 2:  A  (1x)
Keywords :  Retinol Binding, Disease Mutation, Secreted, Sensory Transduction, Vision, Vitamin A, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Wang, R. Connors, P. Fan, X. Wang, Z. Wang, J. Liu, F. Kayser, J. C. Medina, S. Johnstone, H. Xu, S. Thibault, N. Walker, M. Conn, Y. Zhang, Q. Liu, M. P. Grillo, A. Motani, P. Coward, Z. Wang
Structure-Assisted Discovery Of The First Non-Retinoid Ligands For Retinol-Binding Protein 4.
Bioorg. Med. Chem. Lett. V. 24 2885 2014
PubMed-ID: 24835984  |  Reference-DOI: 10.1016/J.BMCL.2014.04.089

(-) Compounds

Molecule 1 - RETINOL-BINDING PROTEIN 4
    Chains: B, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 19-201
    Gene: RBP4, PRO2222
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PLASMA RETINOL-BINDING PROTEIN, PRBP, RBP

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 24)

Asymmetric Unit (3, 24)
No.NameCountTypeFull Name
12WL2Ligand/Ion(1-BENZYL-1H-IMIDAZOL-4-YL)[4-(2-CHLOROPHENYL)PIPERAZIN-1-YL]METHANONE
2EDO20Ligand/Ion1,2-ETHANEDIOL
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
12WL1Ligand/Ion(1-BENZYL-1H-IMIDAZOL-4-YL)[4-(2-CHLOROPHENYL)PIPERAZIN-1-YL]METHANONE
2EDO8Ligand/Ion1,2-ETHANEDIOL
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (3, 14)
No.NameCountTypeFull Name
12WL1Ligand/Ion(1-BENZYL-1H-IMIDAZOL-4-YL)[4-(2-CHLOROPHENYL)PIPERAZIN-1-YL]METHANONE
2EDO12Ligand/Ion1,2-ETHANEDIOL
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:66 , TRP A:67 , PHE B:36 , LEU B:37 , MET B:73 , MET B:88 , TYR B:90 , GLY B:100 , ARG B:121BINDING SITE FOR RESIDUE 2WL B 201
02AC2SOFTWARELYS B:12 , ARG B:19 , TYR B:111 , HOH B:353BINDING SITE FOR RESIDUE PO4 B 202
03AC3SOFTWAREPHE B:9 , ARG B:10 , VAL B:107 , ARG B:155 , GLU B:158BINDING SITE FOR RESIDUE EDO B 203
04AC4SOFTWARESER B:7 , LYS B:85BINDING SITE FOR RESIDUE EDO B 204
05AC5SOFTWAREARG B:153 , ALA B:162 , ARG B:163 , GLN B:164 , TYR B:165BINDING SITE FOR RESIDUE EDO B 205
06AC6SOFTWAREASP B:103 , CYS B:120 , VAL B:169 , HIS B:170 , ASN B:171 , HOH B:351BINDING SITE FOR RESIDUE EDO B 206
07AC7SOFTWAREARG B:166 , LEU B:167 , HOH B:365BINDING SITE FOR RESIDUE EDO B 208
08AC8SOFTWAREARG B:5 , ASP B:126 , ASP B:140 , GLY B:143 , LEU B:144BINDING SITE FOR RESIDUE EDO B 209
09AC9SOFTWAREASP B:108 , THR B:109 , ASP B:110 , TYR B:114 , ILE B:151 , ARG B:155 , HOH B:353 , HOH B:360 , HOH B:367BINDING SITE FOR RESIDUE EDO B 210
10BC1SOFTWARELEU A:35 , PHE A:36 , LEU A:37 , MET A:88 , TYR A:90 , GLY A:100 , ARG A:121 , ASN B:66 , TRP B:67BINDING SITE FOR RESIDUE 2WL A 201
11BC2SOFTWARELYS A:12 , ARG A:19 , TYR A:111BINDING SITE FOR RESIDUE PO4 A 202
12BC3SOFTWAREARG A:153 , GLN A:156 , ARG A:163 , GLN A:164 , TYR A:165BINDING SITE FOR RESIDUE EDO A 203
13BC4SOFTWAREASP A:103 , CYS A:120 , HIS A:170 , HOH A:348 , HOH A:354BINDING SITE FOR RESIDUE EDO A 204
14BC5SOFTWAREPHE A:9 , ARG A:10 , VAL A:107 , ARG A:155 , GLU A:158 , EDO A:213BINDING SITE FOR RESIDUE EDO A 205
15BC6SOFTWAREARG A:5 , ASP A:126 , GLY A:143 , LEU A:144BINDING SITE FOR RESIDUE EDO A 206
16BC7SOFTWAREARG A:163 , ARG A:166BINDING SITE FOR RESIDUE EDO A 207
17BC8SOFTWARETRP A:67 , ASP A:68 , VAL A:69 , CYS A:70 , ASP B:72 , GLY B:92 , VAL B:93 , ALA B:94BINDING SITE FOR RESIDUE EDO A 208
18BC9SOFTWARECYS A:129 , SER A:132 , LEU A:161 , GLN A:164 , HOH A:355BINDING SITE FOR RESIDUE EDO A 209
19CC1SOFTWARELYS A:99 , LYS B:89 , LYS B:99BINDING SITE FOR RESIDUE EDO A 210
20CC2SOFTWARESER A:7 , LYS A:85 , TRP A:105BINDING SITE FOR RESIDUE EDO A 211
21CC3SOFTWARELYS A:29 , LYS A:30 , ASP A:31 , GLN A:164 , ARG A:166BINDING SITE FOR RESIDUE EDO A 212
22CC4SOFTWAREVAL A:11 , VAL A:107 , ASP A:108 , ARG A:155 , EDO A:205BINDING SITE FOR RESIDUE EDO A 213
23CC5SOFTWAREVAL A:42 , THR A:56 , LYS A:58BINDING SITE FOR RESIDUE EDO A 214

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:4 -A:160
2A:70 -A:174
3A:120 -A:129
4B:4 -B:160
5B:70 -B:174
6B:120 -B:129

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4PSQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PSQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PSQ)

(-) Exons   (0, 0)

(no "Exon" information available for 4PSQ)

(-) 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:175
                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhheeeeeeeee........eeeeeeeee.....eeeeeeeeeeee..eeeeeeeeeeeee.....eeeeeeee.......eeeeeeeeee....eeeeeeeeee.....eeeeeeeeee......hhhhhhhhhhhhhhh......ee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4psq A   1 ERDCRVSSFRVKENFDKARFSGTWYAMAKKDPEGLFLQDNIVAEFSVDETGQMSATAKGRVRLLNNWDVCADMVGTFTDTEDPAKFKMKYWGVASFLQKGNDDHWIVDTDYDTYAVQYSCRLLNLDGTCADSYSFVFSRDPNGLPPEAQKIVRQRQEELCLARQYRLIVHNGYCD 175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     


Chain B from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh......hhhhhheeeeeeeee........eeeeeeeee.....eeeeeeeeeeee..eeeeeeeeeeee......eeeeeeee.......eeeeeeeeee....eeeeeeeeee.....eeeeeeeeee......hhhhhhhhhhhhhhh......ee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4psq B   1 ERDCRVSSFRVKENFDKARFSGTWYAMAKKDPEGLFLQDNIVAEFSVDETGQMSATAKGRVRLLNNWDVCADMVGTFTDTEDPAKFKMKYWGVASFLQKGNDDHWIVDTDYDTYAVQYSCRLLNLDGTCADSYSFVFSRDPNGLPPEAQKIVRQRQEELCLARQYRLIVHNGYCD 175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   Legend:   → Mismatch (orange background)
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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 4PSQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PSQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PSQ)

(-) Gene Ontology  (39, 39)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        RET4_HUMAN | P02753: 1brp 1brq 1jyd 1jyj 1qab 1rbp 1rlb 2wq9 2wqa 2wr6 3bsz 3fmz 4o9s

(-) Related Entries Specified in the PDB File

3fmz