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(-) Description

Title :  STRUCTURE OF HERRING TYPE II ANTIFREEZE PROTEIN
 
Authors :  Y. Liu, Z. Li, Q. Lin, J. Seetharaman, J. Sivaraman, C. -L. Hew
Date :  15 May 07  (Deposition) - 26 Jun 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Keywords :  Type Ii Antifreeze Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Liu, Z. Li, Q. Lin, J. Kosinski, J. Seetharaman, J. M. Bujnicki, J. Sivaraman, C. L. Hew
Structure And Evolutionary Origin Of Ca-Dependent Herring Type Ii Antifreeze Protein.
Plos One V. 2 E548 2007
PubMed-ID: 17579720  |  Reference-DOI: 10.1371/JOURNAL.PONE.0000548
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANTIFREEZE PROTEIN TYPE II
    ChainsA, B, C, D, E, F
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System PlasmidPGAPZ ALPHA A
    Expression System Taxid4922
    Expression System Vector TypePLASMID
    GeneHAFP
    Organism CommonATLANTIC HERRING
    Organism ScientificCLUPEA HARENGUS
    Organism Taxid7950

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)A     
Biological Unit 2 (1x) B    
Biological Unit 3 (1x)  C   
Biological Unit 4 (1x)   D  
Biological Unit 5 (1x)    E 
Biological Unit 6 (1x)     F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 6 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:92 , ASP A:94 , GLU A:99 , ASN A:113 , ASP A:114 , HOH A:937BINDING SITE FOR RESIDUE CA A 901
2AC2SOFTWAREGLN B:92 , ASP B:94 , GLU B:99 , ASN B:113 , ASP B:114 , HOH B:978BINDING SITE FOR RESIDUE CA B 902
3AC3SOFTWAREGLN C:92 , ASP C:94 , GLU C:99 , ASN C:113 , ASP C:114 , HOH C:975BINDING SITE FOR RESIDUE CA C 903
4AC4SOFTWAREGLN D:92 , ASP D:94 , GLU D:99 , ASN D:113 , ASP D:114 , HOH D:951BINDING SITE FOR RESIDUE CA D 904
5AC5SOFTWAREGLN E:92 , ASP E:94 , GLU E:99 , ASN E:113 , ASP E:114 , HOH E:932BINDING SITE FOR RESIDUE CA E 905
6AC6SOFTWAREGLN F:92 , ASP F:94 , GLU F:99 , ASN F:113 , ASP F:114 , HOH F:907BINDING SITE FOR RESIDUE CA F 906

(-) SS Bonds  (30, 30)

Asymmetric Unit
No.Residues
1A:4 -A:15
2A:32 -A:125
3A:69 -A:100
4A:89 -A:111
5A:101 -A:117
6B:4 -B:15
7B:32 -B:125
8B:69 -B:100
9B:89 -B:111
10B:101 -B:117
11C:4 -C:15
12C:32 -C:125
13C:69 -C:100
14C:89 -C:111
15C:101 -C:117
16D:4 -D:15
17D:32 -D:125
18D:69 -D:100
19D:89 -D:111
20D:101 -D:117
21E:4 -E:15
22E:32 -E:125
23E:69 -E:100
24E:89 -E:111
25E:101 -E:117
26F:4 -F:15
27F:32 -F:125
28F:69 -F:100
29F:89 -F:111
30F:101 -F:117

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Gln A:92 -Pro A:93
2Gln B:92 -Pro B:93
3Gln C:92 -Pro C:93
4Gln D:92 -Pro D:93
5Gln E:92 -Pro E:93
6Gln F:92 -Pro F:93

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PY2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PY2)

(-) Exons   (0, 0)

(no "Exon" information available for 2PY2)

(-) 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:127
 aligned with Q91992_CLUHA | Q91992 from UniProtKB/TrEMBL  Length:147

    Alignment length:127
                                    30        40        50        60        70        80        90       100       110       120       130       140       
         Q91992_CLUHA    21 CPTDWKMFNGRCFLFNPLQLHWADAQESCMKEGANLASIHSLEESTFVKELTSADLIPSWIGGTDCQVSTRWFWMDSTSMDYADWCAAQPDTTLTECCIQMNVGIGKCWNDTPCTHLHSSICAKPLK 147
               SCOP domains d2py2a_ A: automated matches                                                                                                    SCOP domains
               CATH domains 2py2A00 A:4-130 Mannose-Binding Protein A, subunit A                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eeeeeeeeeehhhhhhhhhhh...ee....hhhhhhhhhh........eeeeee........ee..................hhhh.eeeeee....eeeee.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2py2 A   4 CPTDWKMFNGRCFLFNPLQLHWADAQESCMKEGANLASIHSLEESTFVKELTSADLIPSWIGGTDCQVSTRWFWMDSTSMDYADWCAAQPDTTLTECCIQMNVGIGKCWNDTPCTHLHSSICAKPLK 130
                                    13        23        33        43        53        63        73        83        93       103       113       123       

Chain B from PDB  Type:PROTEIN  Length:127
 aligned with Q91992_CLUHA | Q91992 from UniProtKB/TrEMBL  Length:147

    Alignment length:127
                                    30        40        50        60        70        80        90       100       110       120       130       140       
         Q91992_CLUHA    21 CPTDWKMFNGRCFLFNPLQLHWADAQESCMKEGANLASIHSLEESTFVKELTSADLIPSWIGGTDCQVSTRWFWMDSTSMDYADWCAAQPDTTLTECCIQMNVGIGKCWNDTPCTHLHSSICAKPLK 147
               SCOP domains d2py2b_ B: automated matches                                                                                                    SCOP domains
               CATH domains 2py2B00 B:4-130 Mannose-Binding Protein A, subunit A                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eeeeeeeeeehhhhhhhhhhh...ee....hhhhhhhhhhhh......eeeeee........ee..................hhhh.eeeeee....eeeee.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2py2 B   4 CPTDWKMFNGRCFLFNPLQLHWADAQESCMKEGANLASIHSLEESTFVKELTSADLIPSWIGGTDCQVSTRWFWMDSTSMDYADWCAAQPDTTLTECCIQMNVGIGKCWNDTPCTHLHSSICAKPLK 130
                                    13        23        33        43        53        63        73        83        93       103       113       123       

Chain C from PDB  Type:PROTEIN  Length:127
 aligned with Q91992_CLUHA | Q91992 from UniProtKB/TrEMBL  Length:147

    Alignment length:127
                                    30        40        50        60        70        80        90       100       110       120       130       140       
         Q91992_CLUHA    21 CPTDWKMFNGRCFLFNPLQLHWADAQESCMKEGANLASIHSLEESTFVKELTSADLIPSWIGGTDCQVSTRWFWMDSTSMDYADWCAAQPDTTLTECCIQMNVGIGKCWNDTPCTHLHSSICAKPLK 147
               SCOP domains d2py2c_ C: automated matches                                                                                                    SCOP domains
               CATH domains 2py2C00 C:4-130 Mannose-Binding Protein A, subunit A                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eeeeeeeeeehhhhhhhhhhh...ee....hhhhhhhhhhhh......eeeeee........ee..................hhhh.eeeeee....eeeee.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2py2 C   4 CPTDWKMFNGRCFLFNPLQLHWADAQESCMKEGANLASIHSLEESTFVKELTSADLIPSWIGGTDCQVSTRWFWMDSTSMDYADWCAAQPDTTLTECCIQMNVGIGKCWNDTPCTHLHSSICAKPLK 130
                                    13        23        33        43        53        63        73        83        93       103       113       123       

Chain D from PDB  Type:PROTEIN  Length:127
 aligned with Q91992_CLUHA | Q91992 from UniProtKB/TrEMBL  Length:147

    Alignment length:127
                                    30        40        50        60        70        80        90       100       110       120       130       140       
         Q91992_CLUHA    21 CPTDWKMFNGRCFLFNPLQLHWADAQESCMKEGANLASIHSLEESTFVKELTSADLIPSWIGGTDCQVSTRWFWMDSTSMDYADWCAAQPDTTLTECCIQMNVGIGKCWNDTPCTHLHSSICAKPLK 147
               SCOP domains d2py2d_ D: automated matches                                                                                                    SCOP domains
               CATH domains 2py2D00 D:4-130 Mannose-Binding Protein A, subunit A                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eeeeeeeeeehhhhhhhhhhh...ee....hhhhhhhhhhh.......eeeeee........ee..................hhhh.eeeeee....eeeee.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2py2 D   4 CPTDWKMFNGRCFLFNPLQLHWADAQESCMKEGANLASIHSLEESTFVKELTSADLIPSWIGGTDCQVSTRWFWMDSTSMDYADWCAAQPDTTLTECCIQMNVGIGKCWNDTPCTHLHSSICAKPLK 130
                                    13        23        33        43        53        63        73        83        93       103       113       123       

Chain E from PDB  Type:PROTEIN  Length:127
 aligned with Q91992_CLUHA | Q91992 from UniProtKB/TrEMBL  Length:147

    Alignment length:127
                                    30        40        50        60        70        80        90       100       110       120       130       140       
         Q91992_CLUHA    21 CPTDWKMFNGRCFLFNPLQLHWADAQESCMKEGANLASIHSLEESTFVKELTSADLIPSWIGGTDCQVSTRWFWMDSTSMDYADWCAAQPDTTLTECCIQMNVGIGKCWNDTPCTHLHSSICAKPLK 147
               SCOP domains d2py2e_ E: automated matches                                                                                                    SCOP domains
               CATH domains 2py2E00 E:4-130 Mannose-Binding Protein A, subunit A                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhh........eeeeee........ee..................hhhh.eeeeee....eeeee.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2py2 E   4 CPTDWKMFNGRCFLFNPLQLHWADAQESCMKEGANLASIHSLEESTFVKELTSADLIPSWIGGTDCQVSTRWFWMDSTSMDYADWCAAQPDTTLTECCIQMNVGIGKCWNDTPCTHLHSSICAKPLK 130
                                    13        23        33        43        53        63        73        83        93       103       113       123       

Chain F from PDB  Type:PROTEIN  Length:127
 aligned with Q91992_CLUHA | Q91992 from UniProtKB/TrEMBL  Length:147

    Alignment length:127
                                    30        40        50        60        70        80        90       100       110       120       130       140       
         Q91992_CLUHA    21 CPTDWKMFNGRCFLFNPLQLHWADAQESCMKEGANLASIHSLEESTFVKELTSADLIPSWIGGTDCQVSTRWFWMDSTSMDYADWCAAQPDTTLTECCIQMNVGIGKCWNDTPCTHLHSSICAKPLK 147
               SCOP domains d2py2f_ F: automated matches                                                                                                    SCOP domains
               CATH domains 2py2F00 F:4-130 Mannose-Binding Protein A, subunit A                                                                            CATH domains
           Pfam domains (1) -----------------Lectin_C-2py2F01 F:21-127                                                                                  --- Pfam domains (1)
           Pfam domains (2) -----------------Lectin_C-2py2F02 F:21-127                                                                                  --- Pfam domains (2)
           Pfam domains (3) -----------------Lectin_C-2py2F03 F:21-127                                                                                  --- Pfam domains (3)
           Pfam domains (4) -----------------Lectin_C-2py2F04 F:21-127                                                                                  --- Pfam domains (4)
           Pfam domains (5) -----------------Lectin_C-2py2F05 F:21-127                                                                                  --- Pfam domains (5)
           Pfam domains (6) -----------------Lectin_C-2py2F06 F:21-127                                                                                  --- Pfam domains (6)
         Sec.struct. author .....eee..eeeeeeeeeehhhhhhhhhhh...ee....hhhhhhhhhh........eeeeee........ee..................hhhh.eeeeee....eeeee.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2py2 F   4 CPTDWKMFNGRCFLFNPLQLHWADAQESCMKEGANLASIHSLEESTFVKELTSADLIPSWIGGTDCQVSTRWFWMDSTSMDYADWCAAQPDTTLTECCIQMNVGIGKCWNDTPCTHLHSSICAKPLK 130
                                    13        23        33        43        53        63        73        83        93       103       113       123       

   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, 6)

Asymmetric Unit

(-) CATH Domains  (1, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 6)

Asymmetric Unit
(-)
Clan: C_Lectin (98)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (Q91992_CLUHA | Q91992)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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