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(-) Description

Title :  CRYSTAL STRUCTURE OF AHV_BPA, A BASIC PLA2 FROM AGKISTRODON HALYS PALLAS VENOM
 
Authors :  F. Zeng, L. Niu, X. Li, M. Teng
Date :  07 Oct 12  (Deposition) - 17 Oct 12  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Alpha-Helix, Glycerophospholipid, Venom Gland, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Zeng, L. Niu, X. Li, M. Teng
Crystal Structure Of Ahv_bpa, A Basic Pla2 From Agkistrodon Halys Pallas Venom
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BASIC PHOSPHOLIPASE A2 B
    Chains: A, B, C, D
    EC Number: 3.1.1.4
    Fragment: UNP RESIDUES 17-138
    Organism Common: CHINESE WATER MOCCASIN
    Organism Scientific: GLOYDIUS HALYS
    Organism Taxid: 8714
    Synonym: SVPLA2, BPLA(2), PHOSPHATIDYLCHOLINE 2-ACYLHYDROLASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2CIT2Ligand/IonCITRIC ACID
3G3P2Ligand/IonSN-GLYCEROL-3-PHOSPHATE
4GOL3Ligand/IonGLYCEROL
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CIT2Ligand/IonCITRIC ACID
3G3P1Ligand/IonSN-GLYCEROL-3-PHOSPHATE
4GOL-1Ligand/IonGLYCEROL
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CIT-1Ligand/IonCITRIC ACID
3G3P1Ligand/IonSN-GLYCEROL-3-PHOSPHATE
4GOL3Ligand/IonGLYCEROL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:28 , GLY A:30 , GLY A:32 , ASP A:49BINDING SITE FOR RESIDUE CA A 201
02AC2SOFTWAREARG A:6 , LYS A:7 , LYS A:10 , HOH A:307 , HOH A:360 , HIS C:1 , LEU C:3 , LYS C:7 , ASP C:72BINDING SITE FOR RESIDUE CIT A 202
03AC3SOFTWAREHIS A:1 , LEU A:3 , LYS A:7 , ASP A:72 , HOH A:307 , HOH A:336 , HOH A:378 , ARG C:6 , LYS C:7 , LYS C:10BINDING SITE FOR RESIDUE CIT A 203
04AC4SOFTWAREPHE A:5 , GLY A:30BINDING SITE FOR RESIDUE G3P A 204
05AC5SOFTWARETYR B:28 , GLY B:30 , GLY B:32 , ASP B:49BINDING SITE FOR RESIDUE CA B 201
06AC6SOFTWAREARG B:6 , PRO B:18 , TYR B:22 , ALA B:23 , HOH B:347BINDING SITE FOR RESIDUE GOL B 202
07AC7SOFTWARETYR C:28 , GLY C:30 , GLY C:32 , ASP C:49BINDING SITE FOR RESIDUE CA C 201
08AC8SOFTWARELEU C:2 , PHE C:5 , GLY C:30 , HIS C:48BINDING SITE FOR RESIDUE G3P C 202
09AC9SOFTWAREPRO C:37 , ASP C:39 , ARG C:43BINDING SITE FOR RESIDUE GOL C 203
10BC1SOFTWAREALA C:101 , CYS C:105 , HOH C:306 , HOH C:332 , HOH C:348 , HOH C:358 , HOH C:364BINDING SITE FOR RESIDUE GOL C 204
11BC2SOFTWARETYR D:28 , GLY D:30 , GLY D:32 , ASP D:49BINDING SITE FOR RESIDUE CA D 201

(-) SS Bonds  (28, 28)

Asymmetric Unit
No.Residues
1A:27 -A:126
2A:29 -A:45
3A:44 -A:105
4A:50 -A:133
5A:51 -A:98
6A:61 -A:91
7A:84 -A:96
8B:27 -B:126
9B:29 -B:45
10B:44 -B:105
11B:50 -B:133
12B:51 -B:98
13B:61 -B:91
14B:84 -B:96
15C:27 -C:126
16C:29 -C:45
17C:44 -C:105
18C:50 -C:133
19C:51 -C:98
20C:61 -C:91
21C:84 -C:96
22D:27 -D:126
23D:29 -D:45
24D:44 -D:105
25D:50 -D:133
26D:51 -D:98
27D:61 -D:91
28D:84 -D:96

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4HG9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HG9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HG9)

(-) Exons   (0, 0)

(no "Exon" information available for 4HG9)

(-) 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:122
                                                                                                                                                          
               SCOP domains d4hg9a_ A: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhhhh...........eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hg9 A   1 HLLQFRKMIKKMTGKEPVVSYAFYGCYCGSGGRGKPKDATDRCCFVHDCCYEKVTGCDPKWDDYTYSWKDGDIVCGGDDPCKKEVCECDKAAAICFRDNLKTYKKRYMAYPDILCSSKSEKC 133
                                    10   ||   21        31        41        51    ||||69        79      ||90       100       110       120 ||    131  
                                        14|                                      56|||                 86|                               122|         
                                         16                                       59||                  88                                124         
                                                                                   61|                                                                
                                                                                    67                                                                


Chain B from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains d4hg9b_ B: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhhh...........eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hg9 B   1 HLLQFRKMIKKMTGKEPVVSYAFYGCYCGSGGRGKPKDATDRCCFVHDCCYEKVTGCDPKWDDYTYSWKDGDIVCGGDDPCKKEVCECDKAAAICFRDNLKTYKKRYMAYPDILCSSKSEKC 133
                                    10   ||   21        31        41        51    ||||69        79      ||90       100       110       120 ||    131  
                                        14|                                      56|||                 86|                               122|         
                                         16                                       59||                  88                                124         
                                                                                   61|                                                                
                                                                                    67                                                                


Chain C from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains d4hg9c_ C: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhhhh...........eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hg9 C   1 HLLQFRKMIKKMTGKEPVVSYAFYGCYCGSGGRGKPKDATDRCCFVHDCCYEKVTGCDPKWDDYTYSWKDGDIVCGGDDPCKKEVCECDKAAAICFRDNLKTYKKRYMAYPDILCSSKSEKC 133
                                    10   ||   21        31        41        51    ||||69        79      ||90       100       110       120 ||    131  
                                        14|                                      56|||                 86|                               122|         
                                         16                                       59||                  88                                124         
                                                                                   61|                                                                
                                                                                    67                                                                


Chain D from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains d4hg9d_ D: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhhh...........eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hg9 D   1 HLLQFRKMIKKMTGKEPVVSYAFYGCYCGSGGRGKPKDATDRCCFVHDCCYEKVTGCDPKWDDYTYSWKDGDIVCGGDDPCKKEVCECDKAAAICFRDNLKTYKKRYMAYPDILCSSKSEKC 133
                                    10   ||   21        31        41        51    ||||69        79      ||90       100       110       120 ||    131  
                                        14|                                      56|||                 86|                               122|         
                                         16                                       59||                  88                                124         
                                                                                   61|                                                                
                                                                                    67
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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  (1, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HG9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HG9)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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