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(-) Description

Title :  CRYSTAL STRUCTURE OF ENDOPLASMIC RETICULUM AMINOPEPTIDASE 2 (ERAP2) IN COMPLEX WITH A HYDROXAMIC DERIVATIVE LIGAND
 
Authors :  E. Saridakis, P. Giastas, A. Mpakali, R. Deprez-Poulain, E. Stratikos
Date :  05 Apr 16  (Deposition) - 15 Mar 17  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Endoplasmic Reticulum, Aminopeptidase, Hydrolase, Zn Binding Metallopeptidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Mpakali, P. Giastas, R. Deprez-Poulain, A. Papakyriakou, D. Koumantou, R. Gealageas, S. Tsoukalidou, D. Vourloumis, I. M. Mavridis, E. Stratikos, E. Saridakis
Crystal Structures Of Erap2 Complexed With Inhibitors Revea Pharmacophore Requirements For Optimizing Inhibitor Potency
Acs Med Chem Lett V. 8 333 2017
PubMed-ID: 28337326  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.6B00505

(-) Compounds

Molecule 1 - ENDOPLASMIC RETICULUM AMINOPEPTIDASE 2
    Chains: A, B
    EC Number: 3.4.11.-
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    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  (5, 30)

Asymmetric Unit (5, 30)
No.NameCountTypeFull Name
16GA2Ligand/Ion(2S)-N~1~-BENZYL-2-[(4-FLUOROPHENYL)METHYL]-N~3~-HYDROXYPROPANEDIAMIDE
2BMA3Ligand/IonBETA-D-MANNOSE
3MAN2Ligand/IonALPHA-D-MANNOSE
4NAG21Ligand/IonN-ACETYL-D-GLUCOSAMINE
5ZN2Ligand/IonZINC ION
Biological Unit 1 (3, 14)
No.NameCountTypeFull Name
16GA1Ligand/Ion(2S)-N~1~-BENZYL-2-[(4-FLUOROPHENYL)METHYL]-N~3~-HYDROXYPROPANEDIAMIDE
2BMA1Ligand/IonBETA-D-MANNOSE
3MAN-1Ligand/IonALPHA-D-MANNOSE
4NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (4, 14)
No.NameCountTypeFull Name
16GA1Ligand/Ion(2S)-N~1~-BENZYL-2-[(4-FLUOROPHENYL)METHYL]-N~3~-HYDROXYPROPANEDIAMIDE
2BMA2Ligand/IonBETA-D-MANNOSE
3MAN2Ligand/IonALPHA-D-MANNOSE
4NAG9Ligand/IonN-ACETYL-D-GLUCOSAMINE
5ZN-1Ligand/IonZINC ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:370 , HIS A:374 , GLU A:393 , 6GA A:1015binding site for residue ZN A 1001
02AC2SOFTWAREASP A:198 , GLU A:200 , PRO A:333 , GLY A:334 , ALA A:335 , MET A:336 , GLU A:337 , HIS A:370 , GLU A:371 , HIS A:374 , GLU A:393 , PHE A:450 , TYR A:455 , TYR A:892 , ZN A:1001binding site for residue 6GA A 1015
03AC3SOFTWAREHIS B:370 , HIS B:374 , GLU B:393 , 6GA B:1015binding site for residue ZN B 1001
04AC4SOFTWAREASP B:198 , GLU B:200 , PRO B:333 , ALA B:335 , MET B:336 , GLU B:337 , HIS B:370 , GLU B:371 , HIS B:374 , GLU B:393 , PHE B:450 , TYR B:455 , ZN B:1001binding site for residue 6GA B 1015
05AC5SOFTWAREHIS A:83 , ASN A:85 , GLU A:227 , LEU A:248 , HOH A:1102 , ASP B:291binding site for Poly-Saccharide residues NAG A 1002 through NAG A 1003 bound to ASN A 85
06AC6SOFTWAREASN A:103 , HOH A:1101binding site for Mono-Saccharide NAG A 1010 bound to ASN A 103
07AC7SOFTWAREASN A:119 , ASP A:167binding site for Mono-Saccharide NAG A 1011 bound to ASN A 119
08AC8SOFTWAREHIS A:77 , ASN A:219 , THR A:255 , VAL A:257 , LYS A:258 , TYR A:487 , HOH A:1112 , HOH A:1119binding site for Poly-Saccharide residues NAG A 1004 through BMA A 1006 bound to ASN A 219
09AC9SOFTWAREASN A:294 , ASP A:352 , HOH A:1114binding site for Mono-Saccharide NAG A 1013 bound to ASN A 294
10AD1SOFTWAREASN A:405 , LYS A:466binding site for Poly-Saccharide residues NAG A 1007 through NAG A 1008 bound to ASN A 405
11AD2SOFTWAREASN A:431 , LYS A:545binding site for Mono-Saccharide NAG A 1009 bound to ASN A 431
12AD3SOFTWAREASN A:650binding site for Mono-Saccharide NAG A 1014 bound to ASN A 650
13AD4SOFTWAREASN A:714binding site for Mono-Saccharide NAG A 1012 bound to ASN A 714
14AD5SOFTWAREHIS A:272 , SER A:273 , PRO A:290 , ASP A:291 , ARG A:293 , HOH A:1115 , HIS B:83 , PRO B:84 , ASN B:85 , GLU B:227 , GLY B:246 , LEU B:248binding site for Poly-Saccharide residues NAG B 1002 through MAN B 1006 bound to ASN B 85
15AD6SOFTWAREASN B:103binding site for Mono-Saccharide NAG B 1010 bound to ASN B 103
16AD7SOFTWAREASN B:219 , VAL B:257 , LYS B:258 , HOH B:1101binding site for Poly-Saccharide residues NAG B 1007 through BMA B 1009 bound to ASN B 219
17AD8SOFTWAREASN B:294binding site for Mono-Saccharide NAG B 1011 bound to ASN B 294
18AD9SOFTWAREASN B:405 , ASP B:414 , LYS B:466binding site for Mono-Saccharide NAG B 1012 bound to ASN B 405
19AE1SOFTWAREASN B:431 , LYS B:545 , GLU B:576binding site for Mono-Saccharide NAG B 1013 bound to ASN B 431
20AE2SOFTWAREASN B:650binding site for Mono-Saccharide NAG B 1014 bound to ASN B 650

(-) SS Bonds  (5, 5)

Asymmetric Unit
No.Residues
1A:421 -A:460
2A:503 -A:514
3A:759 -A:766
4B:421 -B:460
5B:759 -B:766

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Lys A:132 -Pro A:133
2Gly A:134 -Lys A:135
3Glu A:200 -Pro A:201
4Leu A:504 -Glu A:505
5Glu A:505 -Ser A:506
6Gly A:511 -Gly A:512
7Leu A:605 -Lys A:606
8Leu A:889 -Gly A:890
9Ala B:56 -Thr B:57
10Lys B:132 -Pro B:133
11Gly B:134 -Lys B:135
12Glu B:200 -Pro B:201

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5J6S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5J6S)

(-) Exons   (0, 0)

(no "Exon" information available for 5J6S)

(-) 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:910
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................eeeeeeeeeeeee....eeeeeeeeeeee.....eeeee....eeeeeeeee..hhhhh......eee.hhhh.eeeee.........eeeeeeeeeee......eeeeeeee.....eeeeeeee....hhhhh...........eeeeeeee....eeee...eeeeee.....eeeee......hhhhh.eeee..eeeeee.....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee......ee....eeeeehhhhh......hhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeehhhhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhhh...eeeeee....eeeeeeee.........hhhhhhhh......eeeeee......eeee....eeeee.......eee.hhhh...eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.........hhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j6s A  53 FPVATNGERFPWQELRLPSVVIPLHYDLFVHPNLTSLDFVASEKIEVLVSNATQFIILHSKDLEITNATLQSEEDSRYMKPGKELKVLSYPAHEQIALLVPEKLTPHLKYYVAMDFQAKLGDGFEGFYKSTYRTLGGETRILAVTDFEPTQARMAFPCFDEPLFKANFSIKIRRESRHIALSNMPKVKTIELEGGLLEDHFETTVKMSTYLVAYIVCDFHSLSGFTSSGVKVSIYASPDKRNQTHYALQASLKLLDFYEKYFDIYYPLSKLDLIAIPDFAPGAMENWGLITYRETSLLFDPKTSSASDKLWVTRVIAHELAHQWFGNLVTMEWWNDIWLNEGFAKYMELIAVNATYPELQFDDYFLNVCFEVITKDSLNSSRPISKPAETPTQIQEMFDEVSYNKGACILNMLKDFLGEEKFQKGIIQYLKKFSYRNAKNDDLWSSLSNSCLESDFTSGGVCHSDPKMTSNMLAFLGENAEVKEMMTTWTLQKGIPLLVVKQDGCSLRLQQERFLQGVFQEDPEWRALQERYLWHIPLTYSTSSSNVIHRHILKSKTDTLDLPEKTSWVKFNVDSNGYYIVHYEGHGWDQLITQLNQNHTLLRPKDRVGLIHDVFQLVGAGRLTLDKALDMTYYLQHETSSPALLEGLSYLESFYHMMDRRNISDISENLKRYLLQYFKPVIDRQSWSDKGSVWDRMLRSALLKLACDLNHAPCIQKAAELFSQWMESSGKLNIPTDVLKIVYSVGAQTTAGWNYLLEQYELSMSSAEQNKILYALSTSKHQEKLLKLIELGMEGKVIKTQNLAALLHAIARRPKGQQLAWDFVRENWTHLLKKFDLGSYDIRMIISGTTAHFSSKDKLQEVKLFFESLEAQGSHLDIFQTVLETITKNIKWLEKNLPTLRTWLMVNTRH 962
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       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       962


Chain B from PDB  Type:PROTEIN  Length:880
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeeeeeeeeeeee....eeeeeeeeeeee......eeee....eeeee..ee..hhhhh......eeeee....eeeee.........eeeeeeeeeee......eeeeeeee.....eeeeeeee....hhhhh...........eeeeeeee....eeee...eeeeee.....eeeee......hhhhh.eeee..eeeeee.....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee.......ee....eeee.hhhh.......hhhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeehhhhhhhhh.......hhhhhhh....eeeeee.......eeeee........hhhhhhhh...........................ee.....................eeeee.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..........hhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhh......hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh......hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j6s B  54 PVATNGERFPWQELRLPSVVIPLHYDLFVHPNLTSLDFVASEKIEVLVSNATQFIILHSKDLEITNATLQSEEDSRYMKPGKELKVLSYPAHEQIALLVPEKLTPHLKYYVAMDFQAKLGDGFEGFYKSTYRTLGGETRILAVTDFEPTQARMAFPCFDEPLFKANFSIKIRRESRHIALSNMPKVKTIELEGGLLEDHFETTVKMSTYLVAYIVCDFHSLSGFTSSGVKVSIYASPDKRNQTHYALQASLKLLDFYEKYFDIYYPLSKLDLIAIPDFAPGAMENWGLITYRETSLLFDPKTSSASDKLWVTRVIAHELAHQWFGNLVTMEWWNDIWLNEGFAKYMELIAVNATYPELQFDDYFLNVCFEVITKDSLNSSRPISKPAETPTQIQEMFDEVSYNKGACILNMLKDFLGEEKFQKGIIQYLKKFSYRNAKNDDLWSSLSNSEVKEMMTTWTLQKGIPLLVVKQDGCSLRLQQERFLQGVFQEDPEWRALQERYLWHIPLTYSTSSSNVIHRHILKSKTDTLDLPEKTSWVKFNVDSNGYYIVHYEGHGWDQLITQLNQNHTLLRPKDRVGLIHDVFQLVGAGRLTLDKALDMTYYLQHETSSPALLEGLSYLESFYHMMDRRNISDISENLKRYLLQYFKPVIDRQSWSDKGSVWDRMLRSALLKLACDLNHAPCIQKAAELFSQWMESSGKLNIPTDVLKIVYSVGAQTTAGWNYLLEQYELSMSSAEQNKILYALSTSKHQEKLLKLIELGMEGKVIKTQNLAALLHAIARRPKGQQLAWDFVRENWTHLLKKFDLGSYDIRMIISGTTAHFSSKDKLQEVKLFFESLEAQGSHLDIFQTVLETITKNIKWLEKNLPTLRTWLMVNTRHH 963
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913       923       933       943       953       963
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          502|                                                                                                                                                                                                                                                                                                                                                                                                                                              
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           533
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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 5J6S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J6S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5J6S)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)

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        ERAP2_HUMAN | Q6P179: 3se6 4e36 4jbs 5ab0 5ab2 5cu5 5k1v

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