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(-) Description

Title :  CRYSTAL STRUCTURE OF THE AAHII-FAB4C1 COMPLEX
 
Authors :  I. P. Fabrichny, G. Mondielli, S. Conrod, M. F. Martin-Eauclaire, Y. Bo P. Marchot
Date :  10 Jan 12  (Deposition) - 07 Mar 12  (Release) - 02 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,H,I,J,L,M,N
Biol. Unit 1:  A,H,L  (1x)
Biol. Unit 2:  B,I,M  (1x)
Biol. Unit 3:  C,J,N  (1x)
Keywords :  Immune System-Toxin Complex, Alpha-Toxin, Conformational Rearrangement, Combining Site, Epitope, Pharmacological Site, Venom, Voltage-Activated Sodium Channel (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. P. Fabrichny, G. Mondielli, S. Conrod, M. F. Martin-Eauclaire, Y. Bourne, P. Marchot
Structural Insights Into Antibody Sequestering And Neutralizing Of Na+-Channel & [Alpha]-Type Modulator From Old-World Scorpion Venom
J. Biol. Chem. V. 287 14136 2012
PubMed-ID: 22371498  |  Reference-DOI: 10.1074/JBC.M111.315382

(-) Compounds

Molecule 1 - ALPHA-MAMMAL TOXIN AAH2
    ChainsA, B, C
    Organism CommonFAT-TAILED SCORPION
    Organism ScientificANDROCTONUS AUSTRALIS HECTOR
    Organism Taxid70175
    SynonymAAH II, AAHII, NEUROTOXIN 2
 
Molecule 2 - FAB ANTIBODY HEAVY CHAIN
    ChainsH, I, J
    FragmentVARIABLE DOMAIN
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 3 - FAB ANTIBODY LIGHT CHAIN
    ChainsL, M, N
    FragmentVARIABLE DOMAIN
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  123456789
Asymmetric Unit ABCHIJLMN
Biological Unit 1 (1x)A  H  L  
Biological Unit 2 (1x) B  I  M 
Biological Unit 3 (1x)  C  J  N

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
2EPE3Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
3NH23Mod. Amino AcidAMINO GROUP
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
3NH21Mod. Amino AcidAMINO GROUP
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
3NH21Mod. Amino AcidAMINO GROUP
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
3NH21Mod. Amino AcidAMINO GROUP

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:13 , LYS A:58 , TYR L:37BINDING SITE FOR RESIDUE CL A1065
2AC2SOFTWARETHR B:13 , LYS B:58 , TYR M:37BINDING SITE FOR RESIDUE CL B1065
3AC3SOFTWARETHR C:13 , LYS C:58 , TYR N:37BINDING SITE FOR RESIDUE CL C1065
4AC4SOFTWARESER I:52 , GLY I:54 , SER I:56BINDING SITE FOR RESIDUE CL I1220
5AC5SOFTWARESER J:52 , GLY J:54 , SER J:56BINDING SITE FOR RESIDUE CL J1219
6AC6SOFTWARESER H:52 , GLY H:54 , SER H:56 , HOH H:2012BINDING SITE FOR RESIDUE CL H1222
7AC7SOFTWARECYS A:16 , GLY A:17 , ARG A:18 , TYR A:21 , SER L:32 , SER M:68BINDING SITE FOR RESIDUE EPE A1066
8AC8SOFTWARECYS B:16 , GLY B:17 , ARG B:18 , TYR B:21 , SER L:68 , SER L:81 , ARG L:82BINDING SITE FOR RESIDUE EPE B1066
9AC9SOFTWARECYS C:16 , GLY C:17 , ARG C:18 , TYR C:21 , SER N:32BINDING SITE FOR RESIDUE EPE C1066

(-) SS Bonds  (24, 24)

Asymmetric Unit
No.Residues
1A:12 -A:63
2A:16 -A:36
3A:22 -A:46
4A:26 -A:48
5B:12 -B:63
6B:16 -B:36
7B:22 -B:46
8B:26 -B:48
9C:12 -C:63
10C:16 -C:36
11C:22 -C:46
12C:26 -C:48
13H:22 -H:96
14H:147 -H:202
15I:22 -I:96
16I:147 -I:202
17J:22 -J:96
18J:147 -J:202
19L:23 -L:93
20L:139 -L:199
21M:23 -M:93
22M:139 -M:199
23N:23 -N:93
24N:139 -N:199

(-) Cis Peptide Bonds  (19, 19)

Asymmetric Unit
No.Residues
1Phe H:153 -Pro H:154
2Glu H:155 -Pro H:156
3Trp H:195 -Pro H:196
4Phe I:153 -Pro I:154
5Glu I:155 -Pro I:156
6Trp I:195 -Pro I:196
7Phe J:153 -Pro J:154
8Glu J:155 -Pro J:156
9Trp J:195 -Pro J:196
10Ser L:7 -Pro L:8
11Val L:99 -Pro L:100
12Tyr L:145 -Pro L:146
13Ser M:7 -Pro M:8
14Val M:99 -Pro M:100
15Tyr M:145 -Pro M:146
16Ser N:7 -Pro N:8
17Val N:99 -Pro N:100
18Ser N:132 -Gly N:133
19Tyr N:145 -Pro N:146

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4AEI)

(-) 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:65
 aligned with SCX2_ANDAU | P01484 from UniProtKB/Swiss-Prot  Length:85

    Alignment length:65
                                    29        39        49        59        69        79     
           SCX2_ANDAU    20 VKDGYIVDDVNCTYFCGRNAYCNEECTKLKGESGYCQWASPYGNACYCYKLPDHVRTKGPGRCHG  84
               SCOP domains d4aeia_ A: Scorpion toxin                                         SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee............hhhhhhhhhhhh...eeeeeeee..eeeeeeeee.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                 4aei A   1 VKDGYIVDDVNCTYFCGRNAYCNEECTKLKGESGYCQWASPYGNACYCYKLPDHVRTKGPGRCHx  65
                                    10        20        30        40        50        60    |
                                                                                           65-NH2

Chain B from PDB  Type:PROTEIN  Length:65
 aligned with SCX2_ANDAU | P01484 from UniProtKB/Swiss-Prot  Length:85

    Alignment length:65
                                    29        39        49        59        69        79     
           SCX2_ANDAU    20 VKDGYIVDDVNCTYFCGRNAYCNEECTKLKGESGYCQWASPYGNACYCYKLPDHVRTKGPGRCHG  84
               SCOP domains d4aeib_ B: Scorpion toxin                                         SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee............hhhhhhhhhhhh...eeeeeeee..eeeeeeeee.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                 4aei B   1 VKDGYIVDDVNCTYFCGRNAYCNEECTKLKGESGYCQWASPYGNACYCYKLPDHVRTKGPGRCHx  65
                                    10        20        30        40        50        60    |
                                                                                           65-NH2

Chain C from PDB  Type:PROTEIN  Length:65
 aligned with SCX2_ANDAU | P01484 from UniProtKB/Swiss-Prot  Length:85

    Alignment length:65
                                    29        39        49        59        69        79     
           SCX2_ANDAU    20 VKDGYIVDDVNCTYFCGRNAYCNEECTKLKGESGYCQWASPYGNACYCYKLPDHVRTKGPGRCHG  84
               SCOP domains d4aeic_ C: Scorpion toxin                                         SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee............hhhhhhhhhhhh...eeeeeeee..eeeeeeeee.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                 4aei C   1 VKDGYIVDDVNCTYFCGRNAYCNEECTKLKGESGYCQWASPYGNACYCYKLPDHVRTKGPGRCHx  65
                                    10        20        30        40        50        60    |
                                                                                           65-NH2

Chain H from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee.........eeeee....eeeeee...hhhhheeeeeee..........ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aei H   1 EVHLVESGGGLVKPGGSLKLSCAASGFTFSGYYMYWVRQTPEKRLEWVASISDGGSFTYYPDSVKGRFTISRDNAKNNLYLQMSSLRSDDTAMYYCSRPDDYSYDGFAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 

Chain I from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee.........eeeee....eeeeee...hhhhheeeeeee..........ee...eeeee........eeeee...eeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeee...........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4aei I   1 EVHLVESGGGLVKPGGSLKLSCAASGFTFSGYYMYWVRQTPEKRLEWVASISDGGSFTYYPDSVKGRFTISRDNAKNNLYLQMSSLRSDDTAMYYCSRPDDYSYDGFAYWGQGTLVTVSAAKTTPPSVYPLAPVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  ||   149       159       169       179       189       199       209       219
                                                                                                                                                              133|                                                                            
                                                                                                                                                               143                                                                            

Chain J from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee.........eeeeehhh.eeeeee...hhhhheeeeeee..........ee...eeeee........eeeee..eeeeeeeee.....eeee.hhh....eee...ee....eeeeeeee...........eeeeeehhhheeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aei J   1 EVHLVESGGGLVKPGGSLKLSCAASGFTFSGYYMYWVRQTPEKRLEWVASISDGGSFTYYPDSVKGRFTISRDNAKNNLYLQMSSLRSDDTAMYYCSRPDDYSYDGFAYWGQGTLVTVSAAKTTPPSVYPLAVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIV 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 ||    150       160       170       180       190       200       210        
                                                                                                                                                             132|                                                                           
                                                                                                                                                              143                                                                           

Chain L from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains d4aeil1 L:1-112 automated matches                                                                               d4aeil2 L:113-218 automated matches                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aei L   1 DVLMTQSPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPNLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        

Chain M from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains d4aeim1 M:1-112 automated matches                                                                               d4aeim2 M:113-217 automated matches                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aei M   1 DVLMTQSPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPNLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       

Chain N from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains d4aein1 N:1-112 automated matches                                                                               d4aein2 N:113-217 automated matches                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee...ee...eeeee.........eeeeeeeeeehhhhhhh.eeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aei N   1 DVLMTQSPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPNLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       

   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  (3, 9)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (SCX2_ANDAU | P01484)
molecular function
    GO:0008200    ion channel inhibitor activity    Stops, prevents, or reduces the activity of an ion channel.
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SCX2_ANDAU | P014841aho 1ptx 1seg

(-) Related Entries Specified in the PDB File

1aho THE AB INITIO STRUCTURE DETERMINATION AND REFINEMENT OF ASCORPION PROTEIN TOXIN
1ptx SCORPION TOXIN II
1seg CRYSTAL STRUCTURE OF A TOXIN CHIMERA BETWEEN LQH-ALPHA -ITFROM THE SCORPION LEIURUS QUINQUESTRIATUS HEBRAEUS ANDAAH2 FROM ANDROCTONUS AUSTRALIS HECTOR
4aeh CRYSTAL STRUCTURE OF THE ANTI-AAHI FAB9C2 ANTIBODY