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(-) Description

Title :  CRYSTAL STRUCTURE OF ERAP2 WITHOUT CATALYTIC ZN(II) ATOM
 
Authors :  E. Saridakis, N. Mathioudakis, P. Giastas, I. M. Mavridis, E. Stratiko
Date :  24 Jul 15  (Deposition) - 23 Sep 15  (Release) - 04 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.02
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Aminopeptidase, Endoplasmic Reticulum, Thermolysin-Like Catalytic Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Mpakali, P. Giastas, N. Mathioudakis, I. M. Mavridis, E. Saridakis E. Stratikos
Structural Basis For Antigenic Peptide Recognition And Processing By Endoplasmic Reticulum (Er) Aminopeptidase 2.
J. Biol. Chem. V. 290 26021 2015
PubMed-ID: 26381406  |  Reference-DOI: 10.1074/JBC.M115.685909

(-) Compounds

Molecule 1 - ENDOPLASMIC RETICULUM AMINOPEPTIDASE 2
    Chains: A, B
    EC Number: 3.4.11.-
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: PFASTBAC-1
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Gene: ERAP2, LRAP
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: LEUKOCYTE-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  (2, 20)

Asymmetric Unit (2, 20)
No.NameCountTypeFull Name
1MAN3Ligand/IonALPHA-D-MANNOSE
2NAG17Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1MAN1Ligand/IonALPHA-D-MANNOSE
2NAG11Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1MAN2Ligand/IonALPHA-D-MANNOSE
2NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:83 , ASN A:85 , GLU A:227 , GLY A:246 , LEU A:248 , HOH A:1164 , HOH A:1168 , HOH A:1177 , ARG B:293binding site for Poly-Saccharide residues NAG A 1001 through MAN A 1003 bound to ASN A 85
02AC2SOFTWAREASN A:103 , HOH A:1175binding site for Mono-Saccharide NAG A 1008 bound to ASN A 103
03AC3SOFTWAREASN A:119binding site for Mono-Saccharide NAG A 1012 bound to ASN A 119
04AC4SOFTWAREHIS A:77 , ASN A:219 , THR A:255 , THR A:256 , VAL A:257 , LYS A:258 , HOH A:1149 , HOH A:1151binding site for Poly-Saccharide residues NAG A 1004 through NAG A 1005 bound to ASN A 219
05AC5SOFTWAREASP A:291 , ARG A:293 , ASN A:294 , HOH A:1103 , HOH A:1162binding site for Mono-Saccharide NAG A 1011 bound to ASN A 294
06AC6SOFTWAREASN A:405 , LYS A:466 , HOH A:1105 , HOH A:1129binding site for Mono-Saccharide NAG A 1006 bound to ASN A 405
07AC7SOFTWAREASN A:431 , HOH A:1158binding site for Mono-Saccharide NAG A 1010 bound to ASN A 431
08AC8SOFTWAREASN A:650binding site for Mono-Saccharide NAG A 1007 bound to ASN A 650
09AC9SOFTWAREASN A:714 , HOH A:1190binding site for Mono-Saccharide NAG A 1009 bound to ASN A 714
10AD1SOFTWAREHIS A:272 , ASP A:291 , ARG A:293 , HIS B:83 , PRO B:84 , ASN B:85 , GLU B:227 , LEU B:248 , HOH B:1147 , HOH B:1154 , HOH B:1172binding site for Poly-Saccharide residues MAN B 1001 through NAG B 1004 bound to ASN B 85
11AD2SOFTWAREHIS B:77 , ASN B:219 , THR B:255 , VAL B:257 , LYS B:258 , TYR B:487binding site for Poly-Saccharide residues NAG B 1005 through NAG B 1006 bound to ASN B 219
12AD3SOFTWAREASN B:294 , HOH B:1159binding site for Mono-Saccharide NAG B 1008 bound to ASN B 294
13AD4SOFTWAREASN B:431 , LYS B:545binding site for Mono-Saccharide NAG B 1007 bound to ASN B 431

(-) 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  (11, 11)

Asymmetric Unit
No.Residues
1Pro A:133 -Gly A:134
2Glu A:200 -Pro A:201
3Leu A:528 -Gly A:529
4Leu A:889 -Gly A:890
5Ser A:926 -His A:927
6Thr B:57 -Asn B:58
7Pro B:133 -Gly B:134
8Glu B:200 -Pro B:201
9Gly B:569 -Val B:570
10Thr B:611 -Leu B:612
11Leu B:889 -Gly B:890

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CU5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CU5)

(-) Exons   (0, 0)

(no "Exon" information available for 5CU5)

(-) 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:871
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeeeeeeeeeeee....eeeeeeeeeeee...eeeeeee....eeeeeeeee.......ee.eeeeehhh.eeeeeeeeee....eeeeeeeeeee......eeeeeeee.....eeeeeeee....hhhhh...........eeeeeeee....eeee...eeeeee.....eeeee......hhhhh.eeee..eeeeee.....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee......ee....eeeee.hhh.......hhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeehhhhhhhhhhh......hhhhhhhhhhh....eeeeeeee..eeeeeeee...............eeeee......eee.....eeeee.......eee.hhhh...eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cu5 A  54 PVATNGERFPWQELRLPSVVIPLHYDLFVHPNLTSLDFVASEKIEVLVSNATQFIILHSKDLEITNATLQSEEYMKPGKELKVLSYPAHEQIALLVPEKLTPHLKYYVAMDFQAKLGDGFEGFYKSTYRTLGGETRILAVTDFEPTQARMAFPCFDEPLFKANFSIKIRRESRHIALSNMPKVKTIELEGGLLEDHFETTVKMSTYLVAYIVCDFHSLSGFTSSGVKVSIYASPDKRNQTHYALQASLKLLDFYEKYFDIYYPLSKLDLIAIPDFAPGAMENWGLITYRETSLLFDPKTSSASDKLWVTRVIAHELAHQWFGNLVTMEWWNDIWLKEGFAKYMELIAVNATYPELQFDDYFLNVCFEVITKDSLNSSRPISKPAETPTQIQEMFDEVSYNKGACILNMLKDFLGEEKFQKGIIQYLKKFSYRNAKNDDLWSSLSNSLGENAEVKEMMTTWTLQKGIPLLVVKQDGCSLRLQQERFLQGVFQERYLWHIPLTYSTSSSNVIHRHILKSKTDTLDLPEKTSWVKFNVDSNGYYIVHYEGHGWDQLITQLNQNHTLLRPKDRVGLIHDVFQLVGAGRLTLDKALDMTYYLQHETSSPALLEGLSYLESFYHMMDRRNISDISENLKRYLLQYFKPVIDRQSWSDKGSVWDRMLRSALLKLACDLNHAPCIQKAAELFSQWMESSGKLNIPTDVLKIVYSVGAQTTAGWNYLLEQYELSMSSAEQNKILYALSTSKHQEKLLKLIELGMEGKVIKTQNLAALLHAIARRPKGQQLAWDFVRENWTHLLKKFDLGSYDIRMIISGTTAHFSSKDKLQEVKLFFESLEAQGSHLDIFQTVLETITKNIKWLEKNLPTLRTWLMVNTR 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       571|      590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960 
                                                                                                  126|                                                                                                                                                                                                                                                                                                                                                                                 502|                                        571|                                                                                                                                                                                                                                                                                                                                                                                            
                                                                                                   130                                                                                                                                                                                                                                                                                                                                                                                  528                                         581                                                                                                                                                                                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:862
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeeeeeeeeeee....eeeeeeeeeeee...eeeeeee....eeeeeeeee......ee.eeeeehhh.eeeeeeeeee....eeeeeeeeeee......eeeeeeee.....eeeeeeee....hhhhh...........eeeeeeee....eeee...eeeeee.....eeeee......hhhhh.eeee..eeeeee.....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee......ee....eeeee.hhh.......hhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeehhhhhhhhhhh...hhhhhhhhhh....eeeeeeee..eeeeeeee............eeeee......eee.....ee..........eee.hhhh...eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cu5 B  55 VATNGERFPWQELRLPSVVIPLHYDLFVHPNLTSLDFVASEKIEVLVSNATQFIILHSKDLEITNATLQSEEDKPGKELKVLSYPAHEQIALLVPEKLTPHLKYYVAMDFQAKLGDGFEGFYKSTYRTLGGETRILAVTDFEPTQARMAFPCFDEPLFKANFSIKIRRESRHIALSNMPKVKTIELEGGLLEDHFETTVKMSTYLVAYIVCDFHSLSGFTSSGVKVSIYASPDKRNQTHYALQASLKLLDFYEKYFDIYYPLSKLDLIAIPDFAPGAMENWGLITYRETSLLFDPKTSSASDKLWVTRVIAHELAHQWFGNLVTMEWWNDIWLKEGFAKYMELIAVNATYPELQFDDYFLNVCFEVITKDSLNSSRPISKPAETPTQIQEMFDEVSYNKGACILNMLKDFLGEEKFQKGIIQYLKKFSYRNAKNDDLWSSLSNSAEVKEMMTTWTLQKGIPLLVVKQDGCSLRLQQERFLQGVRYLWHIPLTYSTSSSNVIHRHILKSKTDTLDLPEKTSWVKFNVDSNGYYIVHYEGHGWDQLITQLNQNHTLLRPKDRVGLIHDVFQLVGAGRLTLDKALDMTYYLQHETSSPALLEGLSYLESFYHMMDRRNISDISENLKRYLLQYFKPVIDRQSWSDKGSVWDRMLRSALLKLACDLNHAPCIQKAAELFSQWMESSGKLNIPTDVLKIVYSVGAQTTAGWNYLLEQYELSMSSAEQNKILYALSTSKHQEKLLKLIELGMEGKVIKTQNLAALLHAIARRPKGQQLAWDFVRENWTHLLKKFDLGSYDIRMIISGTTAHFSSKDKLQEVKLFFESLEAQGSHLDIFQTVLETITKNIKWLEKNLPTLRTWLMVNTR 961
                                    64        74        84        94       104       114       124  ||   138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498   ||  537       547       557       567  ||   589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909       919       929       939       949       959  
                                                                                                  127|                                                                                                                                                                                                                                                                                                                                                                               502|                                   570|                                                                                                                                                                                                                                                                                                                                                                                          
                                                                                                   132                                                                                                                                                                                                                                                                                                                                                                                532                                    583
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  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 5CU5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CU5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CU5)

(-) Gene Ontology  (22, 22)

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  3.4.11.-
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        ERAP2_HUMAN | Q6P179: 3se6 4e36 4jbs 5ab0 5ab2 5j6s 5k1v

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