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(-) Description

Title :  CRYSTAL STRUCTURE OF NPC-BIOTIN-AVIDIN COMPLEX
 
Authors :  T. Terai, E. Maki, S. Sugiyama, Y. Takahashi, H. Matsumura, Y. Mori, T. N
Date :  29 Aug 11  (Deposition) - 28 Dec 11  (Release) - 28 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Beta Barrel, Biotin-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Terai, E. Maki, S. Sugiyama, Y. Takahashi, H. Matsumura, Y. Mori, T. Nagano
Rational Development Of Caged-Biotin Protein-Labeling Agent And Some Applications In Live Cells
Chem. Biol. V. 18 1261 2011
PubMed-ID: 22035795  |  Reference-DOI: 10.1016/J.CHEMBIOL.2011.09.007

(-) Compounds

Molecule 1 - AVIDIN
    ChainsA, B, C, D
    FragmentUNP RESIDUES 25-147
    Organism CommonCHICKEN
    Organism ScientificGALLUS GALLUS
    Organism Taxid9031

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
2NPK4Ligand/Ion5-[(3AS,4R,6AR)-1-{[(1R)-1-(6-NITRO-1,3-BENZODIOXOL-5-YL)ETHOXY]CARBONYL}-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANOIC ACID
3SO46Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:12 , ASP A:13 , LEU A:14 , SER A:16 , TYR A:33 , THR A:35 , VAL A:37 , THR A:38 , ALA A:39 , TRP A:70 , SER A:73 , SER A:75 , TRP A:97 , ILE A:117 , ASN A:118 , HOH A:124 , GLY C:107 , TRP C:110 , HOH C:159BINDING SITE FOR RESIDUE NPK A 1124
02AC2SOFTWARELYS A:9 , GLY A:15 , ASN A:17 , ILE A:34 , LEU A:123BINDING SITE FOR RESIDUE NAG A 1125
03AC3SOFTWAREARG A:2 , LYS A:90 , GLU A:91 , ARG A:122 , HOH A:138 , LYS D:9 , HOH D:173BINDING SITE FOR RESIDUE SO4 A 1126
04AC4SOFTWAREARG A:59 , THR A:60BINDING SITE FOR RESIDUE SO4 A 1127
05AC5SOFTWAREASN B:12 , LEU B:14 , SER B:16 , TYR B:33 , THR B:35 , VAL B:37 , THR B:38 , ALA B:39 , TRP B:70 , SER B:73 , SER B:75 , TRP B:97 , ILE B:117 , ASN B:118 , ILE B:119 , HOH B:142 , HOH B:194 , TRP D:110BINDING SITE FOR RESIDUE NPK B 1124
06AC6SOFTWAREGLY B:15 , ASN B:17 , ILE B:34BINDING SITE FOR RESIDUE NAG B 1125
07AC7SOFTWARELYS B:9 , ARG C:2 , LYS C:90 , GLU C:91 , ARG C:122 , HOH C:149 , HOH C:185BINDING SITE FOR RESIDUE SO4 B 1126
08AC8SOFTWAREARG B:59 , THR B:60 , ARG D:87BINDING SITE FOR RESIDUE SO4 B 1127
09AC9SOFTWAREGLY A:107 , TRP A:110 , ASN C:12 , LEU C:14 , SER C:16 , TYR C:33 , THR C:35 , THR C:38 , ALA C:39 , THR C:40 , TRP C:70 , SER C:75 , TRP C:97 , LEU C:99 , ILE C:117 , ASN C:118 , HOH C:181BINDING SITE FOR RESIDUE NPK C 1124
10BC1SOFTWAREGLY C:15 , ASN C:17BINDING SITE FOR RESIDUE NAG C 1125
11BC2SOFTWAREARG C:59 , THR C:60 , HOH C:154BINDING SITE FOR RESIDUE SO4 C 1127
12BC3SOFTWARETRP B:110 , ASN D:12 , ASP D:13 , LEU D:14 , SER D:16 , TYR D:33 , THR D:35 , VAL D:37 , THR D:38 , ALA D:39 , TRP D:70 , SER D:73 , SER D:75 , TRP D:97 , ILE D:117 , ASN D:118 , ILE D:119 , HOH D:139 , HOH D:167BINDING SITE FOR RESIDUE NPK D 1124
13BC4SOFTWAREGLY D:15 , ASN D:17 , ILE D:34BINDING SITE FOR RESIDUE NAG D 1125
14BC5SOFTWAREARG D:59 , THR D:60 , HOH D:152BINDING SITE FOR RESIDUE SO4 D 1126

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:4 -A:83
2B:4 -B:83
3C:4 -C:83
4D:4 -D:83

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3VHM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 4)

Asymmetric/Biological Unit (1, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_AVID_CHICK_001 *I58TAVID_CHICK  ---  ---A/B/C/DI34T
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 6)

Asymmetric/Biological Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AVIDIN_2PS51326 Avidin-like domain profile.AVID_CHICK26-149
 
  2A:2-123
C:2-123
2AVIDIN_1PS00577 Avidin-like domain signature.AVID_CHICK132-146
 
 
 
  4A:108-122
B:108-122
C:108-122
D:108-122

(-) Exons   (4, 16)

Asymmetric/Biological Unit (4, 16)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSGALT000000038551ENSGALE00000024242Z:8485802-848588281AVID_CHICK1-27274A:1-3
B:3-3
C:1-3
D:3-3
3
1
3
1
1.4ENSGALT000000038554ENSGALE00000024240Z:8501440-8501650211AVID_CHICK28-98714A:4-74
B:4-74
C:4-74
D:4-74
71
71
71
71
1.5ENSGALT000000038555ENSGALE00000024243Z:8502076-8502196121AVID_CHICK98-138414A:74-114
B:74-114
C:74-114
D:74-114
41
41
41
41
1.6aENSGALT000000038556aENSGALE00000024241Z:8502284-8502409126AVID_CHICK138-152154A:114-123
B:114-123
C:114-123
D:114-123
10
10
10
10

(-) 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:123
 aligned with AVID_CHICK | P02701 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:123
                                    34        44        54        64        74        84        94       104       114       124       134       144   
           AVID_CHICK    25 ARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 147
               SCOP domains d3vhma_ A: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.....eeee.......eeeeeee............eeeeeee.hhhhh...eeeeee.......eeeeeeeeee.....eeeeeeeeee....hhhhhhh.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------T----------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -AVIDIN_2  PDB: A:2-123 UniProt: 26-149                                                                                     PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------AVIDIN_1       - PROSITE (2)
           Transcript 1 (1) 1.1Exon 1.4  PDB: A:4-74 UniProt: 28-98                                   ---------------------------------------Exon 1.6a  Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------Exon 1.5  PDB: A:74-114 UniProt: 98-138  --------- Transcript 1 (2)
                 3vhm A   1 ARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 123
                                    10        20        30        40        50        60        70        80        90       100       110       120   

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with AVID_CHICK | P02701 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:121
                                    36        46        56        66        76        86        96       106       116       126       136       146 
           AVID_CHICK    27 KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 147
               SCOP domains d3vhmb_ B: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.....eeee.......eeeeeee............eeeeeee.hhhhh...eeeeeee......eeeeeeeeee.....eeeeeeeeee....hhhhhhh.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------T----------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) AVIDIN_2  PDB: - UniProt: 26-149                                                                                          PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------AVIDIN_1       - PROSITE (2)
           Transcript 1 (1) 1Exon 1.4  PDB: B:4-74 UniProt: 28-98                                   ---------------------------------------Exon 1.6a  Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------Exon 1.5  PDB: B:74-114 UniProt: 98-138  --------- Transcript 1 (2)
                 3vhm B   3 KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 123
                                    12        22        32        42        52        62        72        82        92       102       112       122 

Chain C from PDB  Type:PROTEIN  Length:123
 aligned with AVID_CHICK | P02701 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:123
                                    34        44        54        64        74        84        94       104       114       124       134       144   
           AVID_CHICK    25 ARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 147
               SCOP domains d3vhmc_ C: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.....eeee.......eeeeeee............eeeeeee.hhhhh...eeeeeee......eeeeeeeeee.....eeeeeeeeee....hhhhhhh.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------T----------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -AVIDIN_2  PDB: C:2-123 UniProt: 26-149                                                                                     PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------AVIDIN_1       - PROSITE (2)
           Transcript 1 (1) 1.1Exon 1.4  PDB: C:4-74 UniProt: 28-98                                   ---------------------------------------Exon 1.6a  Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------Exon 1.5  PDB: C:74-114 UniProt: 98-138  --------- Transcript 1 (2)
                 3vhm C   1 ARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 123
                                    10        20        30        40        50        60        70        80        90       100       110       120   

Chain D from PDB  Type:PROTEIN  Length:121
 aligned with AVID_CHICK | P02701 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:121
                                    36        46        56        66        76        86        96       106       116       126       136       146 
           AVID_CHICK    27 KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 147
               SCOP domains d3vhmd_ D: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.....eeee.......eeeeeee............eeeeeee.hhhhh...eeeeeee......eeeeeeeeee.....eeeeeeeeee....hhhhhhh.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------T----------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) AVIDIN_2  PDB: - UniProt: 26-149                                                                                          PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------AVIDIN_1       - PROSITE (2)
           Transcript 1 (1) 1Exon 1.4  PDB: D:4-74 UniProt: 28-98                                   ---------------------------------------Exon 1.6a  Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------Exon 1.5  PDB: D:74-114 UniProt: 98-138  --------- Transcript 1 (2)
                 3vhm D   3 KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 123
                                    12        22        32        42        52        62        72        82        92       102       112       122 

   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  (1, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VHM)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (AVID_CHICK | P02701)
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.

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  3vhm
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  AVID_CHICK | P02701
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 Related Entries

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

UniProtKB/Swiss-Prot
        AVID_CHICK | P027011avd 1ave 1ij8 1ldo 1ldq 1lel 1nqn 1rav 1vyo 2a5b 2a5c 2a8g 2avi 2c4i 2cam 2jgs 2mf6 3fdc 3mm0 3vgw 3vhh 3vhi 4i60 4jhq 4u46 5chk 5hlm 5iru 5irw

(-) Related Entries Specified in the PDB File

3vgw 3vhh 3vhi