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(-) Description

Title :  CRYSTAL STRUCTURE OF LS24, A SEED ALBUMIN FROM LATHYRUS SATIVUS
 
Authors :  V. Gaur, I. A. Qureshi, A. Singh, V. Chanana, D. M. Salunke
Date :  05 Feb 10  (Deposition) - 23 Feb 10  (Release) - 21 Apr 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Seed Albumin, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. Gaur, I. A. Qureshi, A. Singh, V. Chanana, D. M. Salunke
Crystal Structure And Functional Insights Of Hemopexin Fold Protein From Grass Pea
Plant Physiol. V. 152 1842 2010
PubMed-ID: 20147493  |  Reference-DOI: 10.1104/PP.109.150680

(-) Compounds

Molecule 1 - LS-24
    ChainsA, B, C, D
    FragmentPLANT HEMOPEXIN DOMAIN
    Organism ScientificLATHYRUS SATIVUS
    Organism Taxid3860
    Other DetailsSEEDS

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 25)

Asymmetric Unit (5, 25)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2CL4Ligand/IonCHLORIDE ION
3NA4Ligand/IonSODIUM ION
4SPM1Ligand/IonSPERMINE
5UNK12Mod. Amino Acid
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3NA-1Ligand/IonSODIUM ION
4SPM-1Ligand/IonSPERMINE
5UNK-1Mod. Amino Acid
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3NA-1Ligand/IonSODIUM ION
4SPM1Ligand/IonSPERMINE
5UNK-1Mod. Amino Acid

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:7 , ASP A:65 , ASP A:121 , ASP A:175 , HOH A:232BINDING SITE FOR RESIDUE CA A 310
02AC2SOFTWAREALA A:9 , SER A:67 , ALA A:123 , ALA A:177BINDING SITE FOR RESIDUE CL A 314
03AC3SOFTWAREASP A:69 , TYR A:124 , ARG A:125 , PHE A:178 , ALA A:179 , HOH A:242BINDING SITE FOR RESIDUE NA A 318
04AC4SOFTWARETHR B:1 , ASN B:7 , ASP B:65 , ASP B:121 , ASP B:175 , HOH B:308BINDING SITE FOR RESIDUE CA B 311
05AC5SOFTWAREALA B:9 , SER B:67 , ALA B:123 , ALA B:177BINDING SITE FOR RESIDUE CL B 315
06AC6SOFTWAREASP B:69 , ARG B:125 , ALA B:179BINDING SITE FOR RESIDUE NA B 319
07AC7SOFTWARETHR C:1 , ASN C:7 , ASP C:65 , ASP C:121 , ASP C:175 , HOH C:317BINDING SITE FOR RESIDUE CA C 312
08AC8SOFTWAREALA C:9 , SER C:67 , ALA C:123 , ALA C:177BINDING SITE FOR RESIDUE CL C 316
09AC9SOFTWAREASP C:69 , TYR C:124 , ARG C:125 , PHE C:178 , ALA C:179 , HOH C:326BINDING SITE FOR RESIDUE NA C 320
10BC1SOFTWAREASN D:7 , ASP D:65 , ASP D:121 , ASP D:175 , HOH D:446BINDING SITE FOR RESIDUE CA D 313
11BC2SOFTWAREALA D:9 , SER D:67 , ALA D:123 , ALA D:177BINDING SITE FOR RESIDUE CL D 317
12BC3SOFTWAREASP D:69 , TYR D:124 , ARG D:125 , PHE D:178 , ALA D:179 , HOH D:455BINDING SITE FOR RESIDUE NA D 321
13BC4SOFTWAREGLU B:80 , HOH B:244 , HOH B:332 , ASN D:81 , SER D:118 , HOH D:282 , HOH D:435 , HOH D:436BINDING SITE FOR RESIDUE SPM D 230

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LP9)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Gly A:43 -Pro A:44
2Gly A:100 -Pro A:101
3Val A:225 -Pro A:226
4Gly B:43 -Pro B:44
5Gly B:100 -Pro B:101
6Val B:225 -Pro B:226
7Gly C:43 -Pro C:44
8Gly C:100 -Pro C:101
9Val C:225 -Pro C:226
10Gly D:43 -Pro D:44
11Gly D:100 -Pro D:101
12Val D:225 -Pro D:226

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LP9)

(-) PROSITE Motifs  (1, 16)

Asymmetric Unit (1, 16)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEMOPEXIN_2PS51642 Hemopexin repeat profile.ALB2_LATSA3-46
 
 
 
61-111
 
 
 
117-165
 
 
 
171-221
 
 
 
  16A:3-46
B:3-46
C:3-46
D:3-46
A:61-111
B:61-111
C:61-111
D:61-111
A:117-165
B:117-165
C:117-165
D:117-165
A:171-221
B:171-221
C:171-221
D:171-221
Biological Unit 1 (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEMOPEXIN_2PS51642 Hemopexin repeat profile.ALB2_LATSA3-46
 
 
 
61-111
 
 
 
117-165
 
 
 
171-221
 
 
 
  8A:3-46
-
C:3-46
-
A:61-111
-
C:61-111
-
A:117-165
-
C:117-165
-
A:171-221
-
C:171-221
-
Biological Unit 2 (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEMOPEXIN_2PS51642 Hemopexin repeat profile.ALB2_LATSA3-46
 
 
 
61-111
 
 
 
117-165
 
 
 
171-221
 
 
 
  8-
B:3-46
-
D:3-46
-
B:61-111
-
D:61-111
-
B:117-165
-
D:117-165
-
B:171-221
-
D:171-221

(-) Exons   (0, 0)

(no "Exon" information available for 3LP9)

(-) 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:227
 aligned with ALB2_LATSA | D4AEP7 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:227
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       
           ALB2_LATSA     1 TKPGYINAAFRSSKNNEAYFFINDKYVLLDYAPGSSRDKVLYGPTPVRDGFKSLNQTIFGSYGIDCSFDTENNEAFIFYENFCALIDYAPHSKKDKIILGPKKIADVFPFFEGTVFESGIDAAYRSTRGKEVYLFKGDQYARIDYGSNSMVNKEIKSISSGYPCFRNTIFESGADAAFASHKTNEVYFFKDDHYARVKVTPGGKLAIMDGVREIVDYWPSLKDIVPL 227
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee.....eeeeee..eeeeee........eeeeeeeehhhhhhhhh.hhhhhhh..eeee....eeeeee..eeeeee........eeeeeeeehhhhhhhhh.........eeee.....eeeeee..eeeeee....ee.....eehhhhhhhhh.hhhhhh..eeee.....eeeeee..eeeeee.......ee....eehhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --HEMOPEXIN_2  PDB: A:3-46 UniProt: 3-46      --------------HEMOPEXIN_2  PDB: A:61-111 UniProt: 61-111         -----HEMOPEXIN_2  PDB: A:117-165 UniProt: 117-165     -----HEMOPEXIN_2  PDB: A:171-221 UniProt: 171-221       ------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lp9 A   1 TKPGYINAAFRSSKNNEAYFFINDKYVLLDYAPGSSRDKVLYGPTPVRDGFKSLNQTIFGSYGIDCSFDTENNEAFIFYENFCALIDYAPHSKKDKIILGPKKIADVFPFFEGTVFESGIDAAYRSTRGKEVYLFKGDQYARIDYGSNSMVNKEIKSISSGYPCFRNTIFESGADAAFASHKTNEVYFFKDDHYARVKVTPxxKLxIMDGVREIVDYWPSLKDIVPL 227
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 ||  | 210       220       
                                                                                                                                                                                                                                   202-UNK                     
                                                                                                                                                                                                                                    203-UNK                    
                                                                                                                                                                                                                                       206-UNK                 

Chain B from PDB  Type:PROTEIN  Length:227
 aligned with ALB2_LATSA | D4AEP7 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:227
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       
           ALB2_LATSA     1 TKPGYINAAFRSSKNNEAYFFINDKYVLLDYAPGSSRDKVLYGPTPVRDGFKSLNQTIFGSYGIDCSFDTENNEAFIFYENFCALIDYAPHSKKDKIILGPKKIADVFPFFEGTVFESGIDAAYRSTRGKEVYLFKGDQYARIDYGSNSMVNKEIKSISSGYPCFRNTIFESGADAAFASHKTNEVYFFKDDHYARVKVTPGGKLAIMDGVREIVDYWPSLKDIVPL 227
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee.....eeeeee..eeeeee........eeeeeeeehhhhhhhhh.hhhhhhh..eeee....eeeeee..eeeeee........eeeeeeeehhhhhhhhh.........eeee.....eeeeee..eeeeee...........eehhhhhhhhh.hhhhhh..eeee.....eeeeee..eeeeee.......ee....eehhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --HEMOPEXIN_2  PDB: B:3-46 UniProt: 3-46      --------------HEMOPEXIN_2  PDB: B:61-111 UniProt: 61-111         -----HEMOPEXIN_2  PDB: B:117-165 UniProt: 117-165     -----HEMOPEXIN_2  PDB: B:171-221 UniProt: 171-221       ------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lp9 B   1 TKPGYINAAFRSSKNNEAYFFINDKYVLLDYAPGSSRDKVLYGPTPVRDGFKSLNQTIFGSYGIDCSFDTENNEAFIFYENFCALIDYAPHSKKDKIILGPKKIADVFPFFEGTVFESGIDAAYRSTRGKEVYLFKGDQYARIDYGSNSMVNKEIKSISSGYPCFRNTIFESGADAAFASHKTNEVYFFKDDHYARVKVTPxxKLxIMDGVREIVDYWPSLKDIVPL 227
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 ||  | 210       220       
                                                                                                                                                                                                                                   202-UNK                     
                                                                                                                                                                                                                                    203-UNK                    
                                                                                                                                                                                                                                       206-UNK                 

Chain C from PDB  Type:PROTEIN  Length:227
 aligned with ALB2_LATSA | D4AEP7 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:227
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       
           ALB2_LATSA     1 TKPGYINAAFRSSKNNEAYFFINDKYVLLDYAPGSSRDKVLYGPTPVRDGFKSLNQTIFGSYGIDCSFDTENNEAFIFYENFCALIDYAPHSKKDKIILGPKKIADVFPFFEGTVFESGIDAAYRSTRGKEVYLFKGDQYARIDYGSNSMVNKEIKSISSGYPCFRNTIFESGADAAFASHKTNEVYFFKDDHYARVKVTPGGKLAIMDGVREIVDYWPSLKDIVPL 227
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee.....eeeeee..eeeeee........eeeeeeeehhhhhhhhh.hhhhhhh..eeee....eeeeee..eeeeee........eeeeeeeehhhhhhhhh.........eeee.....eeeeee..eeeeee....ee.....eehhhhhhhhh.........eeee.....eeeeee..eeeeee.............eehhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --HEMOPEXIN_2  PDB: C:3-46 UniProt: 3-46      --------------HEMOPEXIN_2  PDB: C:61-111 UniProt: 61-111         -----HEMOPEXIN_2  PDB: C:117-165 UniProt: 117-165     -----HEMOPEXIN_2  PDB: C:171-221 UniProt: 171-221       ------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lp9 C   1 TKPGYINAAFRSSKNNEAYFFINDKYVLLDYAPGSSRDKVLYGPTPVRDGFKSLNQTIFGSYGIDCSFDTENNEAFIFYENFCALIDYAPHSKKDKIILGPKKIADVFPFFEGTVFESGIDAAYRSTRGKEVYLFKGDQYARIDYGSNSMVNKEIKSISSGYPCFRNTIFESGADAAFASHKTNEVYFFKDDHYARVKVTPxxKLxIMDGVREIVDYWPSLKDIVPL 227
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 ||  | 210       220       
                                                                                                                                                                                                                                   202-UNK                     
                                                                                                                                                                                                                                    203-UNK                    
                                                                                                                                                                                                                                       206-UNK                 

Chain D from PDB  Type:PROTEIN  Length:227
 aligned with ALB2_LATSA | D4AEP7 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:227
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       
           ALB2_LATSA     1 TKPGYINAAFRSSKNNEAYFFINDKYVLLDYAPGSSRDKVLYGPTPVRDGFKSLNQTIFGSYGIDCSFDTENNEAFIFYENFCALIDYAPHSKKDKIILGPKKIADVFPFFEGTVFESGIDAAYRSTRGKEVYLFKGDQYARIDYGSNSMVNKEIKSISSGYPCFRNTIFESGADAAFASHKTNEVYFFKDDHYARVKVTPGGKLAIMDGVREIVDYWPSLKDIVPL 227
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Hemopexin-3lp9D01 D:175-223                      ---- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Hemopexin-3lp9D02 D:175-223                      ---- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Hemopexin-3lp9D03 D:175-223                      ---- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Hemopexin-3lp9D04 D:175-223                      ---- Pfam domains (4)
           Pfam domains (5) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Hemopexin-3lp9D05 D:175-223                      ---- Pfam domains (5)
           Pfam domains (6) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Hemopexin-3lp9D06 D:175-223                      ---- Pfam domains (6)
           Pfam domains (7) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Hemopexin-3lp9D07 D:175-223                      ---- Pfam domains (7)
           Pfam domains (8) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Hemopexin-3lp9D08 D:175-223                      ---- Pfam domains (8)
           Pfam domains (9) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Hemopexin-3lp9D09 D:175-223                      ---- Pfam domains (9)
          Pfam domains (10) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Hemopexin-3lp9D10 D:175-223                      ---- Pfam domains (10)
          Pfam domains (11) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Hemopexin-3lp9D11 D:175-223                      ---- Pfam domains (11)
          Pfam domains (12) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Hemopexin-3lp9D12 D:175-223                      ---- Pfam domains (12)
         Sec.struct. author .....eeeeee.....eeeeee..eeeeee........eeeeeeeehhhhhhhhh.hhhhhhh..eeee....eeeeee..eeeeee........eeeeeeeehhhhhhhhh.........eeee.....eeeeee..eeeeee....ee.....eehhhhhhhhh.........eeee.....eeeeee..eeeeee.......ee....eehhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --HEMOPEXIN_2  PDB: D:3-46 UniProt: 3-46      --------------HEMOPEXIN_2  PDB: D:61-111 UniProt: 61-111         -----HEMOPEXIN_2  PDB: D:117-165 UniProt: 117-165     -----HEMOPEXIN_2  PDB: D:171-221 UniProt: 171-221       ------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lp9 D   1 TKPGYINAAFRSSKNNEAYFFINDKYVLLDYAPGSSRDKVLYGPTPVRDGFKSLNQTIFGSYGIDCSFDTENNEAFIFYENFCALIDYAPHSKKDKIILGPKKIADVFPFFEGTVFESGIDAAYRSTRGKEVYLFKGDQYARIDYGSNSMVNKEIKSISSGYPCFRNTIFESGADAAFASHKTNEVYFFKDDHYARVKVTPxxKLxIMDGVREIVDYWPSLKDIVPL 227
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 ||  | 210       220       
                                                                                                                                                                                                                                   202-UNK                     
                                                                                                                                                                                                                                    203-UNK                    
                                                                                                                                                                                                                                       206-UNK                 

   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 3LP9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LP9)

(-) Pfam Domains  (1, 12)

Asymmetric Unit

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (ALB2_LATSA | D4AEP7)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0045735    nutrient reservoir activity    Functions in the storage of nutritious substrates.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3LP9)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3LP9)