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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN ENDOPLASMIC RETICULUM AMINOPEPTIDASE 2 IN COMPLEX WITH PHOSPHINIC PSEUDOTRIPEPTIDE INHIBITOR.
 
Authors :  E. Saridakis, J. Birtley, E. Stratikos, I. M. Mavridis
Date :  20 Feb 13  (Deposition) - 11 Dec 13  (Release) - 25 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.79
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Thermolysin-Like Catalytic Domain, Hydrolase, Aminopeptidase, Zinc Binding, Endoplasmic Reticulum, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Zervoudi, E. Saridakis, J. R. Birtley, S. S. Seregin, E. Reeves, P. Kokkala, Y. A. Aldhamen, A. Amalfitano, I. M. Mavridis, E. James, D. Georgiadis, E. Stratikos
Rationally Designed Inhibitor Targeting Antigen-Trimming Aminopeptidases Enhances Antigen Presentation And Cytotoxic T-Cell Responses.
Proc. Natl. Acad. Sci. Usa V. 110 19890 2013
PubMed-ID: 24248368  |  Reference-DOI: 10.1073/PNAS.1309781110

(-) Compounds

Molecule 1 - ENDOPLASMIC RETICULUM AMINOPEPTIDASE 2
    ChainsA, B
    EC Number3.4.11.-
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System PlasmidPFASTBAC-1
    Expression System Taxid7111
    Expression System Vector TypeBACULOVIRUS
    GeneERAP2, LRAP
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymLEUKOCYTE-DERIVED ARGININE AMINOPEPTIDASE, L-RAP

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 21)

Asymmetric Unit (5, 21)
No.NameCountTypeFull Name
1IMD2Ligand/IonIMIDAZOLE
2MAN2Ligand/IonALPHA-D-MANNOSE
3NAG13Ligand/IonN-ACETYL-D-GLUCOSAMINE
4P522Ligand/IonNALPHA-[(2S)-2-{[[(1R)-1-AMINO-3-PHENYLPROPYL](HYDROXY)PHOSPHORYL]METHYL}-4-METHYLPENTANOYL]-L-TRYPTOPHANAMIDE
5ZN2Ligand/IonZINC ION
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1IMD2Ligand/IonIMIDAZOLE
2MAN-1Ligand/IonALPHA-D-MANNOSE
3NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE
4P521Ligand/IonNALPHA-[(2S)-2-{[[(1R)-1-AMINO-3-PHENYLPROPYL](HYDROXY)PHOSPHORYL]METHYL}-4-METHYLPENTANOYL]-L-TRYPTOPHANAMIDE
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 9)
No.NameCountTypeFull Name
1IMD-1Ligand/IonIMIDAZOLE
2MAN2Ligand/IonALPHA-D-MANNOSE
3NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
4P521Ligand/IonNALPHA-[(2S)-2-{[[(1R)-1-AMINO-3-PHENYLPROPYL](HYDROXY)PHOSPHORYL]METHYL}-4-METHYLPENTANOYL]-L-TRYPTOPHANAMIDE
5ZN-1Ligand/IonZINC ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:83 , ASN A:85 , ARG A:226 , GLU A:227 , NAG A:1002 , HOH A:1257 , HOH A:1283BINDING SITE FOR RESIDUE NAG A 1001
02AC2SOFTWAREGLY A:246 , NAG A:1001 , HOH A:1174 , HOH A:1257BINDING SITE FOR RESIDUE NAG A 1002
03AC3SOFTWAREASN A:219 , VAL A:257 , LYS A:258 , NAG A:1004BINDING SITE FOR RESIDUE NAG A 1003
04AC4SOFTWARENAG A:1003 , HOH A:1220BINDING SITE FOR RESIDUE NAG A 1004
05AC5SOFTWAREASN A:405 , ASP A:414 , HOH A:1243 , HOH A:1254BINDING SITE FOR RESIDUE NAG A 1005
06AC6SOFTWAREASN A:650BINDING SITE FOR RESIDUE NAG A 1006
07AC7SOFTWAREASN A:103 , HOH A:1197 , HOH A:1217 , HOH A:1249BINDING SITE FOR RESIDUE NAG A 1007
08AC8SOFTWAREHIS A:370 , HIS A:374 , GLU A:393 , P52 A:1009BINDING SITE FOR RESIDUE ZN A 1008
09AC9SOFTWAREARG A:293 , MAN B:1002 , NAG B:1004 , HOH B:1175BINDING SITE FOR RESIDUE MAN B 1001
10BC1SOFTWAREMAN B:1001BINDING SITE FOR RESIDUE MAN B 1002
11BC2SOFTWAREHIS B:83 , PRO B:84 , ASN B:85 , GLU B:227 , LEU B:248 , NAG B:1004 , HOH B:1116BINDING SITE FOR RESIDUE NAG B 1003
12BC3SOFTWAREHIS A:272 , ASP A:291 , GLY B:246 , MAN B:1001 , NAG B:1003BINDING SITE FOR RESIDUE NAG B 1004
13BC4SOFTWAREGLU A:200 , GLY A:334 , ALA A:335 , GLU A:337 , ARG A:366 , VAL A:367 , HIS A:370 , GLU A:371 , HIS A:374 , LYS A:392 , GLU A:393 , PHE A:450 , TYR A:455 , TYR A:892 , ZN A:1008 , HOH A:1232 , HOH A:1244BINDING SITE FOR RESIDUE P52 A 1009
14BC5SOFTWAREHIS A:708 , ARG A:865 , HOH A:1123BINDING SITE FOR RESIDUE IMD A 1010
15BC6SOFTWAREVAL A:152 , GLU A:154 , LEU A:156BINDING SITE FOR RESIDUE IMD A 1011
16BC7SOFTWAREASN B:219 , VAL B:257 , LYS B:258 , TYR B:487 , NAG B:1006 , HOH B:1173BINDING SITE FOR RESIDUE NAG B 1005
17BC8SOFTWARENAG B:1005BINDING SITE FOR RESIDUE NAG B 1006
18BC9SOFTWAREASN B:431 , HOH B:1165BINDING SITE FOR RESIDUE NAG B 1007
19CC1SOFTWAREASN B:294BINDING SITE FOR RESIDUE NAG B 1008
20CC2SOFTWAREHIS B:370 , HIS B:374 , GLU B:393 , P52 B:1010BINDING SITE FOR RESIDUE ZN B 1009
21CC3SOFTWAREGLU B:200 , ALA B:335 , GLU B:337 , HIS B:370 , GLU B:371 , LYS B:392 , GLU B:393 , PHE B:450 , TYR B:455 , TYR B:892 , ZN B:1009 , HOH B:1141 , HOH B:1146BINDING SITE FOR RESIDUE P52 B 1010

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:421 -A:460
2A:759 -A:766
3B:421 -B:460
4B:759 -B:766

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Ala A:56 -Thr A:57
2Pro A:133 -Gly A:134
3Glu A:200 -Pro A:201
4Leu A:528 -Gly A:529
5Leu A:889 -Gly A:890
6Ser A:926 -His A:927
7Thr B:57 -Asn B:58
8Asn B:58 -Gly B:59
9Glu B:200 -Pro B:201
10Gly B:569 -Val B:570
11Glu B:582 -Arg B:583
12Leu B:889 -Gly B:890

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JBS)

(-) 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:869
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4jbsa1 A:54-271 automated matches                                                                                                                                                                                     d4jbsa2 A:272-546 automated matches                                                                                                                                                                                                                       d4jbsa3 A:547-637 automated matches                                             d4jbsa4 A:638-961 automated matches                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeeeeeeeeeeee....eeeeeeeeeeee.....eeeee....eeeeeeeee.......ee.eeeeehhh.eeeee.........eeeeeeeeeee......eeeeeeee.....eeeeeeee....hhhhh...........eeeeeeee....eeee...eeeeee.....eeeee......hhhhh.eeee..eeeeee.....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee......ee....eeeeehhhhh......hhhhhhhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeehhhhhhhhhhh......hhhhhhhhhhhh...eeeeeeee..eeeeeeee.............eee........eee.....eeeee..........hhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jbs A  54 PVATNGERFPWQELRLPSVVIPLHYDLFVHPNLTSLDFVASEKIEVLVSNATQFIILHSKDLEITNATLQSEEYMKPGKELKVLSYPAHEQIALLVPEKLTPHLKYYVAMDFQAKLGDGFEGFYKSTYRTLGGETRILAVTDFEPTQARMAFPCFDEPLFKANFSIKIRRESRHIALSNMPKVKTIELEGGLLEDHFETTVKMSTYLVAYIVCDFHSLSGFTSSGVKVSIYASPDKRNQTHYALQASLKLLDFYEKYFDIYYPLSKLDLIAIPDFAPGAMENWGLITYRETSLLFDPKTSSASDKLWVTRVIAHELAHQWFGNLVTMEWWNDIWLKEGFAKYMELIAVNATYPELQFDDYFLNVCFEVITKDSLNSSRPISKPAETPTQIQEMFDEVSYNKGACILNMLKDFLGEEKFQKGIIQYLKKFSYRNAKNDDLWSSLSNSLGENAEVKEMMTTWTLQKGIPLLVVKQDGCSLRLQQERFLQGQERYLWHIPLTYSTSSSNVIHRHILKSKTDTLDLPEKTSWVKFNVDSNGYYIVHYEGHGWDQLITQLNQNHTLLRPKDRVGLIHDVFQLVGAGRLTLDKALDMTYYLQHETSSPALLEGLSYLESFYHMMDRRNISDISENLKRYLLQYFKPVIDRQSWSDKGSVWDRMLRSALLKLACDLNHAPCIQKAAELFSQWMESSGKLNIPTDVLKIVYSVGAQTTAGWNYLLEQYELSMSSAEQNKILYALSTSKHQEKLLKLIELGMEGKVIKTQNLAALLHAIARRPKGQQLAWDFVRENWTHLLKKFDLGSYDIRMIISGTTAHFSSKDKLQEVKLFFESLEAQGSHLDIFQTVLETITKNIKWLEKNLPTLRTWLMVNTR 961
                                    63        73        83        93       103       113       123  ||   136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496     ||531       541       551       561       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952         
                                                                                                  126|                                                                                                                                                                                                                                                                                                                                                                                 502|                                      569|                                                                                                                                                                                                                                                                                                                                                                                            
                                                                                                   130                                                                                                                                                                                                                                                                                                                                                                                  528                                       581                                                                                                                                                                                                                                                                                                                                                                                            

Chain B from PDB  Type:PROTEIN  Length:854
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4jbsb1 B:55-271 automated matches                                                                                                                                                                                d4jbsb2 B:272-546 automated matches                                                                                                                                                                                                                   d4jbsb3 B:547-637 automated matches                                       d4jbsb4 B:638-961 automated matches                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................eeeeeeeee....eeeeeeeee........eeeee....eeeeeeeee...ee.eeeee....eeeee..........eeeeeeeeee......eeeeeeee.....eeeeeeee....hhhhh.........eeeeeeeeee....eeee...eeeeee.....eeeee.....ee.hhh.eeee..eeeeee.....eeeeee...hhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee......ee....eeeee...........hhhhhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhh.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..eeehhhhhhhhhhh....hhhhhhhhh...............................................................hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jbs B  55 VATNGERFPWQELRLPSVVIPLHYDLFVHPNLTSLDFVASEKIEVLVSNATQFIILHSKDLEITNATLQSEPGKELKVLSYPAHEQIALLVPEKLTPHLKYYVAMDFQAKLGDGFEGFYKSTYRTLGGETRILAVTDFEPTQARMAFPCFDEPLFKANFSIKIRRESRHIALSNMPKVKTIELEGGLLEDHFETTVKMSTYLVAYIVCDFHSLSGFTSSGVKVSIYASPDKRNQTHYALQASLKLLDFYEKYFDIYYPLSKLDLIAIPDFAPGAMENWGLITYRETSLLFDPKTSSASDKLWVTRVIAHELAHQWFGNLVTMEWWNDIWLKEGFAKYMELIAVNATYPELQFDDYFLNVCFEVITKDSLNSSRPISKPAETPTQIQEMFDEVSYNKGACILNMLKDFLGEEKFQKGIIQYLKKFSYRNAKNDDLWSSLSNSAEVKEMMTTWTLQKGIPLLDGCSLRLQQERFLQGVERYLWHIPLTTSSSNVIHRHILKSKTDTLDLPEKTSWVKFNVDSNGYYIVHYEGHGWDQLITQLNQNHTLLRPKDRVGLIHDVFQLVGAGRLTLDKALDMTYYLQHETSSPALLEGLSYLESFYHMMDRRNISDISENLKRYLLQYFKPVIDRQSWSDKGSVWDRMLRSALLKLACDLNHAPCIQKAAELFSQWMESSGKLNIPTDVLKIVYSVGAQTTAGWNYLLEQYELSMSSAEQNKILYALSTSKHQEKLLKLIELGMEGKVIKTQNLAALLHAIARRPKGQQLAWDFVRENWTHLLKKFDLGSYDIRMIISGTTAHFSSKDKLQEVKLFFESLEAQGSHLDIFQTVLETITKNIKWLEKNLPTLRTWLMVNTR 961
                                    64        74        84        94       104       114       124||     141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501||     540       550|      564     ||585     ||597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917       927       937       947       957    
                                                                                                125|                                                                                                                                                                                                                                                                                                                                                                              502|               550|            570|      591|                                                                                                                                                                                                                                                                                                                                                                               
                                                                                                 133                                                                                                                                                                                                                                                                                                                                                                               532                555             582       594                                                                                                                                                                                                                                                                                                                                                                               

   Legend:   → Mismatch (orange background)
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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  (4, 8)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    Glu B:200 - Pro B:201   [ RasMol ]  
    Glu B:582 - Arg B:583   [ RasMol ]  
    Gly B:569 - Val B:570   [ RasMol ]  
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    Leu A:889 - Gly A:890   [ RasMol ]  
    Leu B:889 - Gly B:890   [ RasMol ]  
    Pro A:133 - Gly A:134   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        ERAP2_HUMAN | Q6P1793se6 4e36 5ab0 5ab2 5cu5 5j6s 5k1v

(-) Related Entries Specified in the PDB File

3se6 THE SAME PROTEIN (392N VARIANT) UNCOMPLEXED
4e36 THE SAME PROTEIN (392K VARIANT) UNCOMPLEXED