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(-) Description

Title :  THE C2B DOMAIN OF RABPHILIN 3A IN COMPLEX WITH PI(4,5)P2
 
Authors :  C. Ferrer-Orta, N. Verdaguer
Date :  08 Aug 16  (Deposition) - 21 Jun 17  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Vesicle Fusion, Pip2, C2 Domain, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Ferrer-Orta, T. Coronado-Parra, M. D. Perez-Sanchez, C. Silva, D. Lopez-Martinez, J. Baltanas-Copado, J. C. Gomez-Fernandez, S. Corbalan-Garcia, N. Verdaguer
The Rabphilin 3A-Snap25 Interactions: A New Piece To The Synaptic Puzzle
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RABPHILIN-3A
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Taxid: 511693
    Fragment: C2B DOMAIN, UNP RESIDUES 536-680
    Gene: RPH3A
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: EXOPHILIN-1

 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, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2GOL7Ligand/IonGLYCEROL
3PIO2Ligand/Ion[(2R)-2-OCTANOYLOXY-3-[OXIDANYL-[(1R,2R,3S,4R,5R,6S)-2,3,6-TRIS(OXIDANYL)-4,5-DIPHOSPHONOOXY-CYCLOHEXYL]OXY-PHOSPHORYL]OXY-PROPYL] OCTANOATE
4SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL4Ligand/IonGLYCEROL
3PIO1Ligand/Ion[(2R)-2-OCTANOYLOXY-3-[OXIDANYL-[(1R,2R,3S,4R,5R,6S)-2,3,6-TRIS(OXIDANYL)-4,5-DIPHOSPHONOOXY-CYCLOHEXYL]OXY-PHOSPHORYL]OXY-PROPYL] OCTANOATE
4SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL3Ligand/IonGLYCEROL
3PIO1Ligand/Ion[(2R)-2-OCTANOYLOXY-3-[OXIDANYL-[(1R,2R,3S,4R,5R,6S)-2,3,6-TRIS(OXIDANYL)-4,5-DIPHOSPHONOOXY-CYCLOHEXYL]OXY-PHOSPHORYL]OXY-PROPYL] OCTANOATE
4SO4-1Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMET A:570 , ASP A:571 , ASP A:631 , ASP A:633 , ASP A:639binding site for residue CA A 701
02AC2SOFTWAREASP A:571 , ASP A:577 , ASP A:631 , TYR A:632 , ASP A:633 , SO4 A:707binding site for residue CA A 702
03AC3SOFTWAREASN A:608 , GLU A:610binding site for residue GOL A 703
04AC4SOFTWAREHIS A:594 , LYS A:595 , THR A:602 , ASN A:604 , PRO A:605 , GLU A:606binding site for residue GOL A 704
05AC5SOFTWAREASN A:677 , ASN A:679 , GLN B:676 , ASN B:677 , GLU B:678binding site for residue GOL A 705
06AC6SOFTWAREGLU A:606 , GLU A:609 , GLU A:610binding site for residue GOL A 706
07AC7SOFTWAREGLN A:553 , ASP A:571 , ASP A:633 , ILE A:634 , GLY A:635 , CA A:702binding site for residue SO4 A 707
08AC8SOFTWARETYR A:575 , LYS A:581 , LYS A:590 , LYS A:595 , LYS A:601 , HIS A:617 , TYR A:659 , LEU A:662 , LYS A:663 , ASN A:664 , SER B:618 , ALA B:621 , ILE B:648 , SER B:649 , TYR B:659binding site for residue PIO A 708
09AC9SOFTWAREASP B:571 , ASP B:577 , ASP B:631 , TYR B:632 , ASP B:633binding site for residue CA B 701
10AD1SOFTWAREMET B:570 , ASP B:571 , ASP B:631 , ASP B:633 , ASP B:639binding site for residue CA B 702
11AD2SOFTWARESER A:649 , TRP B:630 , SER B:637 , ASN B:638binding site for residue GOL B 703
12AD3SOFTWAREMET B:570binding site for residue GOL B 705
13AD4SOFTWARELYS A:622 , TYR B:550 , LYS B:581 , LYS B:590 , LYS B:595 , LYS B:601 , HIS B:617 , SER B:618 , ASN B:638 , HOH B:802binding site for residues GOL B 704 and PIO B 706

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LO8)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys B:585 -Pro B:586

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LO8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LO8)

(-) Exons   (0, 0)

(no "Exon" information available for 5LO8)

(-) 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:140
                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee....eeeeeeeeee............eeeeeee.hhh....eee..........eeeeeeee..hhhhhh...eeeeeee.......eeeeeeee.....hhhhhhhhhhhhh....eeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lo8 A 540 ERGKILVSLMYSTQQGGLIVGIIRCVHLAAMDANGYSDPFVKLWLKPDMGKKAKHKTQIKKKTLNPEFNEEFFYDIKHSDLAKKSLDISVWDYDIGKSNDYIGGCQLGISAKGERLKHWYECLKNKDKKIERWHQLQNEN 679
                                   549       559       569       579       589       599       609       619       629       639       649       659       669       679


Chain B from PDB  Type:PROTEIN  Length:142
                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee....eeeeeeeeee............eeeeeeee.......eee..........eeeeeeee..hhhhhh..eeeeeeee.......eeeeeeee......hhhhhhhhhhhh....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lo8 B 537 DIEERGKILVSLMYSTQQGGLIVGIIRCVHLAAMDANGYSDPFVKLWLKPDMGKKAKHKTQIKKKTLNPEFNEEFFYDIKHSDLAKKSLDISVWDYDIGKSNDYIGGCQLGISAKGERLKHWYECLKNKDKKIERWHQLQNE 678
                                   546       556       566       576       586       596       606       616       626       636       646       656       666       676
   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 5LO8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LO8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LO8)

(-) Gene Ontology  (34, 34)

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    Lys B:585 - Pro B:586   [ RasMol ]  
 
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        RP3A_RAT | P47709: 1zbd 2chd 2cm5 2cm6 3rpb 4lt7 4np9 4ns0 5lob 5low

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