ISB Project Page for Kwokleung Chan


My protein is 1ANX:  Annexin V
Calcium/Phospholipid-Binding Protein
(PDB,SCOP,CATH,PDBsum,Pfam,InterPro,PROSITE)
This protein is an anticoagulant protein that acts as an indirect inhibitor of the thromboplastin-specific complex, which is invloved in the blood coagulation cascade.
The annexins are a family of proteins that bind to phospholipids in a calcium-dependent manner [MEDLINE:91266960]. The binding is specific for calcium and for acidic phospholipids. Annexins have been claimed to be involved in cytoskeletal interactions, phospholipase inhibition, intracellular signalling, anticoagulation, and membrane fusion.

PDB   from RCSB
There are three SO4 ligands are twelve Ca metal ions.

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Resolution [Å]: 2.50 R-Value: 0.198
Space Group: P 1  
Unit Cell:
dim [Å]: a 91.20 b 91.30 c 36.20
angles [°]: alpha 82.40 beta 82.40 gamma 118.20
 
Polymer Chains: A, B, C Residues: 957
Atoms: 7936
The crystals are triclinic (P1) with three molecules per asymmetric unit and pseudo-R3 symmetry, reflecting a tendency of annexin to form trimers.

Ligand Information (SO4, from PDBsum)
Chain A, ligand residue: SO4 322

Chain B, ligand residue: SO4 322

Chain C ligand residue: SO4 322




Sctuctural Classification of Protein

Lineage:

  1. Root: scop
  2. Class: All alpha proteins
  3. Fold: Annexin
    5 helices; folded leaf, closed
  4. Superfamily: Annexin
    duplication: consists of four domains of the same fold
  5. Family: Annexin
  6. Protein: Annexin V
  7. Species: Human (Homo sapiens)
Annexin V, together with Annexin I, III, IV, VI, XII and 24 (Ca32) belong to the Annexin Family.  Fold Annexin has only the Annexin Superfamily, which has only the Annexin Family.

CATH


 Mainly Alpha level Mainly Alpha

Orthogonal Bundle level Orthogonal Bundle

Annexin V, domain 1 level Annexin V, domain 1

CALCIUM/PHOSPHOLIPID-BINDING PROTEIN level CALCIUM/PHOSPHOLIPID-BINDING PROTEIN

CALCIUM/PHOSPHOLIPID-BINDING PROTEIN level
CALCIUM/PHOSPHOLIPID-BINDING PROTEIN

Domain CATH code Length Image
Domain 1
1anxA1 1.10.220.10 73
1anxB1 1.10.220.10 73
1anxC1 1.10.220.10 73
Domain 2
1anxA2 1.10.220.10 74
1anxB2 1.10.220.10 74
1anxC2 1.10.220.10 74
Domain 3
1anxA3
 1.10.220.10
 86
1anxB3
 1.10.220.10
 86
1anxC3
 1.10.220.10
 86
Domain 4
1anxA4 1.10.220.10 72
1anxB4 1.10.220.10 72
1anxC4 1.10.220.10 72
Domains 1,3: CALCIUM/PHOSPHOLIPID BINDING
Domains 2,4: PHOSPHOLIPID ANALOG
Under the Homologous Superfamily CALCIUM/PHOSPHOLIPID-BINDING PROTEIN, all are either calcium/phospholipid-binding, metal binding, phospholipid analog, metal transport, or metal, lipid binding protiein.

DSSP Sequence and secondary structure

    S = Bend
    T = Single Turn (minimum helix is defined at 2 n-turns)
    B = Single Bridge (ladders of length 1)
    G = 310-helix (3-helix)
    H = a-helix  (4-helix)
    S = disulfide bond
    E = extended ladders (b-strands)

Chain 1ANX:A

Compound Annexin V - Chain A
Type Protein    
Molecular Weight 35791    
Number of Residues 319    
Number of Alpha 21 Content of Alpha 69.59
Number of Beta 0 Content of Beta 0.00 


   1 AQVLRGTVTD FPGFDERADA ETLRKAMKGL GTDEESILTL LTSRSNAQRQ 
        S  S     TT  HHHHH HHHHHHHSSS S  HHHHHHH HTSS HHHHH 

  51 EISAAFKTLF GRDLLDDLKS ELTGKFEKLI VALMKPSRLY DAYELKHALK 
     HHHHHHHHHH S  HHHHHHH HTTHHHHHHH HHHHTTHHHH THHHHHHHH  

 101 GAGTNEKVLT EIIASRTPEE LRAIKQVYEE EYGSSLEDDV VGDTSGYYQR 
     SSS  HHHHH HHHHHTTHHH HHHHHHHHHH HHSS HHHHH HHHTTHHHHH 

 151 MLVVLLQANR DPDAGIDEAQ VEQDAQALFQ AGELKWGTDE EKFITIFGTR 
     HHHHHHT           HHH HHHHHHHHHH HTTTSSS  H HHHHHHHHHT 

 201 SVSHLRKVFD KYMTISGFQI EETIDRETSG NLEQLLLAVV KSIRSIPAYL 
     THHHHHHHHH HHHHHHSS H HHHHHHHTTH HHHHHHHHHH HHHHTHHHHH 

 251 AETLYYAMKG AGTDDHTLIR VMVSRSEIDL FNIRKEFRKN FATSLYSMIK 
     HHHHHGGGSS SS  HHHHHH HHHHHTTTTH HHHHHHHHHS SSS HHHHHH 

 301 GDTSGDYKKA LLLLCGEDD 
     HHTTHHHHHH HHHHH

Chain 1ANX:B

Compound Annexin V - Chain B
Type Protein    
Molecular Weight 35791    
Number of Residues 319    
Number of Alpha 21 Content of Alpha 69.59
Number of Beta 0 Content of Beta 0.00


Sequence and secondary structure

   1 AQVLRGTVTD FPGFDERADA ETLRKAMKGL GTDEESILTL LTSRSNAQRQ 
        S  S     TT  HHHHH HHHHHHHSSS S  HHHHHHH HTSS HHHHH 

  51 EISAAFKTLF GRDLLDDLKS ELTGKFEKLI VALMKPSRLY DAYELKHALK 
     HHHHHHHHHH S  HHHHHHH HTTHHHHHHH HHHHTTHHHH THHHHHHHH  

 101 GAGTNEKVLT EIIASRTPEE LRAIKQVYEE EYGSSLEDDV VGDTSGYYQR 
     TTS  HHHHH HHHHHTTHHH HHHHHHHHHH HHSS HHHHH HHHTTHHHHH 

 151 MLVVLLQANR DPDAGIDEAQ VEQDAQALFQ AGELKWGTDE EKFITIFGTR 
     HHHHHHTT          HHH HHHHHHHHHH HTTSSSS  H HHHHHHHHHT 

 201 SVSHLRKVFD KYMTISGFQI EETIDRETSG NLEQLLLAVV KSIRSIPAYL 
     THHHHHHHHH HHHHHHSS H HHHHHHHTTH HHHHHHHHHH HHHHTHHHHH 

 251 AETLYYAMKG AGTDDHTLIR VMVSRSEIDL FNIRKEFRKN FATSLYSMIK 
     HHHHHTTSSS SS  HHHHHH HHHHHTTTTH HHHHHHHHHT TSS HHHHHH 

 301 GDTSGDYKKA LLLLCGEDD 
     HHTTHHHHHH HHHHH

Chain 1ANX:C

Compound Annexin V - Chain C
Type Protein    
Molecular Weight 35791    
Number of Residues 319    
Number of Alpha 21 Content of Alpha 68.97
Number of Beta 0 Content of Beta 0.00

Sequence and secondary structure

   1 AQVLRGTVTD FPGFDERADA ETLRKAMKGL GTDEESILTL LTSRSNAQRQ 
        S  S     TT  HHHHH HHHHHHHSSS S  HHHHHHH HTSS HHHHH 

  51 EISAAFKTLF GRDLLDDLKS ELTGKFEKLI VALMKPSRLY DAYELKHALK 
     HHHHHHHHHH S  HHHHHHH HTTHHHHHHH HHHHTTHHHH THHHHHHHS  

 101 GAGTNEKVLT EIIASRTPEE LRAIKQVYEE EYGSSLEDDV VGDTSGYYQR 
     SSS  HHHHH HHHHHTTHHH HHHHHHHHHH HHSS HHHHH HHHTTHHHHH 

 151 MLVVLLQANR DPDAGIDEAQ VEQDAQALFQ AGELKWGTDE EKFITIFGTR 
     HHHHHHTT          HHH HHHHHHHHHH HTTSSSS  H HHHHHHHHHT 

 201 SVSHLRKVFD KYMTISGFQI EETIDRETSG NLEQLLLAVV KSIRSIPAYL 
     THHHHHHHHH HHHHHHSS H HHHHHHHTTH HHHHHHHHHH HHHHTHHHHH 

 251 AETLYYAMKG AGTDDHTLIR VMVSRSEIDL FNIRKEFRKN FATSLYSMIK 
     HHHHHTTSSS SS  HHHHHH HHHHHHTTTH HHHHHHHHHT TSS HHHHHH 

 301 GDTSGDYKKA LLLLCGEDD 
     TTTTHHHHHH HHHHH

From PDBsum

. Chain A ( 316 residues )

structural classification ( 4 domains) :
Domain Links CATH no.   Class Architecture
1 1.10.220.10 -> Mainly Alpha Orthogonal Bundle
2 " " ->      "        "      "        "
3 " " ->      "        "      "        "
4 " " ->      "        "      "        "
Secondary structure plot



. Chain B ( 316 residues )

structural classification ( 4 domains) :
Domain Links CATH no.   Class Architecture
1 1.10.220.10 -> Mainly Alpha Orthogonal Bundle
2 " " ->      "        "      "        "
3 " " ->      "        "      "        "
4 " " ->      "        "      "        "
Secondary structure plot

. Chain C ( 316 residues )

structural classification ( 4 domains) :
Domain Links CATH no.   Class Architecture
1 1.10.220.10 -> Mainly Alpha Orthogonal Bundle
2 " " ->      "        "      "        "
3 " " ->      "        "      "        "
4 " " ->      "        "      "        "
Secondary structure plot




Structural Neighbor by CE (search)

Criteria used: Z-Score>4.0 RMSD<3.0Å Sequence identity<40.0%
Results: 1DK5:A, 1DK5:B
Z-Score=7.5, RMSD=2.4Å, Sequence identity=31.8%, Aligned=308/322, Gaps=8 





  1ANX:A    5/7     RGTVTDF-PGFDERADAETLRKAMKGLGTDEESILTLLTSRSNAQRQEISAAFKTLFGRD
  1DK5:A    9/10    MASLTVPAHVPSAAEDCEQLRSAFKGWGTNEKLIISILAHRTAAQRKLIRQTYAETFGED


  1ANX:A   64/66    LLDDLKSELTGKFEKLIVALMKPSRLYDAYELKHALKGAGTNEKVLTEIIASRTPEELRA
  1DK5:A   69/70    LLKELDRELTHDFEKLVLVWTLDPSERDAHLAKEATKRWTKSNFVLVELACTRSPKELVL


  1ANX:A  124/126   IKQVYEEEYGSSLEDDVVGDTSGYYQRMLVVLLQANRDPDAGIDEAQVEQDAQALFQAGE
  1DK5:A  129/130   AREAYHARYKKSLEEDVAYHTTGDHRKLLVPLVSSYRYGGEEVDLRLAKAESKILHEKIS


  1ANX:A  184/186   LKWGTD--EEKFITIFGTRSVSHLRKVFDKYMTISGFQIEETIDRETSGNLEQLLLAVVK
  1DK5:A  189/190   ---DKAYSDDEVIRILATRSKAQLNATLNHYKDEHGEDILKQLED--GDEFVALLRATIK


  1ANX:A  242/244   SIRSIPAYLAETLYYAMKGAGTDDHTLIRVMVSRSEIDLFNIRKEFRKNFATSLYSMIKG
  1DK5:A  244/245   GLVYPEHYFVEVLRDAINRRGTEEDHLTRVIATRAEVDLKIIADEYQKRDSIPLGRAIAK


  1ANX:A  302/304   DTSGDYKKALLLLCGE
  1DK5:A  304/305   DTRGDYESMLLALLGQ


CLUSTAL W (1.82) multiple sequence alignment



1ANX_A          -----AQVLRGTVTDFPGFDERADAETLRKAMKGLGTDEESILTLLTSRSNAQRQEISAA 55
1DK5_A          MAHHHHHHMASLTVPAHVPSAAEDCEQLRSAFKGWGTNEKLIISILAHRTAAQRKLIRQT 60
                      : : . ..     .   *.* **.*:** **:*: *:::*: *: ***: *  :

1ANX_A          FKTLFGRDLLDDLKSELTGKFEKLIVALMKPSRLYDAYELKHALKGAGTNEKVLTEIIAS 115
1DK5_A          YAETFGEDLLKELDRELTHDFEKLVLVWTLDPSERDAHLAKEATKRWTKSNFVLVELACT 120
                :   **.***.:*. *** .****::.    .   **:  *.* *   ..: **.*: .:

1ANX_A          RTPEELRAIKQVYEEEYGSSLEDDVVGDTSGYYQRMLVVLLQANRDPDAGIDEAQVEQDA 175
1DK5_A          RSPKELVLAREAYHARYKKSLEEDVAYHTTGDHRKLLVPLVSSYRYGGEEVDLRLAKAES 180
                *:*:**   ::.*. .* .***:**. .*:* ::::** *:.: *  .  :*   .: ::

1ANX_A          QALFQAGELKWGTDEEKFITIFGTRSVSHLRKVFDKYMTISGFQIEETIDRETSGNLEQL 235
1DK5_A          KILHEKISDKAYSDDE-VIRILATRSKAQLNATLNHYKDEHGEDILKQLE--DGDEFVAL 237
                : *.:  . *  :*:* .* *:.*** ::*. .:::*    * :* : ::   ..::  *

1ANX_A          LLAVVKSIRSIPAYLAETLYYAMKGAGTDDHTLIRVMVSRSEIDLFNIRKEFRKNFATSL 295
1DK5_A          LRATIKGLVYPEHYFVEVLRDAINRRGTEEDHLTRVIATRAEVDLKIIADEYQKRDSIPL 297
                * *.:*.:     *:.*.*  *::  **::. * **:.:*:*:**  * .*::*. : .*

1ANX_A          YSMIKGDTSGDYKKALLLLCGEDD- 319
1DK5_A          GRAIAKDTRGDYESMLLALLGQEED 322
                   *  ** ***:. ** * *:::
The alignment given by CLUSTALW agrees very well with that from CE.