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(-) Description

Title :  HUMAN AMINOPEPTIDASE N (CD13) IN COMPLEX WITH BESTATIN
 
Authors :  A. H. Wong, J. M. Rini
Date :  05 Jul 12  (Deposition) - 05 Sep 12  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Metalloprotease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. H. Wong, D. Zhou, J. M. Rini
The X-Ray Crystal Structure Of Human Aminopeptidase N Reveals A Novel Dimer And The Basis For Peptide Processing.
J. Biol. Chem. V. 287 36804 2012
PubMed-ID: 22932899  |  Reference-DOI: 10.1074/JBC.M112.398842

(-) Compounds

Molecule 1 - AMINOPEPTIDASE N
    Chains: A
    EC Number: 3.4.11.2
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Taxid: 9606
    Gene: ANPEP, APN, CD13, PEPN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: AP-N, HAPN, ALANYL AMINOPEPTIDASE, AMINOPEPTIDASE M, AP-M, MICROSOMAL AMINOPEPTIDASE, MYELOID PLASMA MEMBRANE GLYCOPROTEIN CD13, GP150

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 25)

Asymmetric Unit (6, 25)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2BES1Ligand/Ion2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID
3BMA1Ligand/IonBETA-D-MANNOSE
4NAG11Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SO410Ligand/IonSULFATE ION
6ZN1Ligand/IonZINC ION
Biological Unit 1 (5, 48)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2BES2Ligand/Ion2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID
3BMA2Ligand/IonBETA-D-MANNOSE
4NAG22Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SO420Ligand/IonSULFATE ION
6ZN-1Ligand/IonZINC ION

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:128 , GLY A:184 , GLU A:185 , HOH A:1465 , HOH A:1543 , HOH A:1775BINDING SITE FOR RESIDUE NAG A 1001
02AC2SOFTWARESER A:84 , TYR A:85 , ARG A:86 , ASN A:234 , THR A:271 , NAG A:1003 , HOH A:1658 , HOH A:1975 , HOH A:2018BINDING SITE FOR RESIDUE NAG A 1002
03AC3SOFTWAREARG A:110 , NAG A:1002 , BMA A:1004 , HOH A:2018BINDING SITE FOR RESIDUE NAG A 1003
04AC4SOFTWARENAG A:1003 , HOH A:1586BINDING SITE FOR RESIDUE BMA A 1004
05AC5SOFTWAREHIS A:239 , LYS A:241 , LEU A:243 , SER A:255 , PRO A:257 , ASN A:265 , HOH A:1233 , HOH A:1961 , HOH A:2006 , HOH A:2025BINDING SITE FOR RESIDUE NAG A 1005
06AC6SOFTWARETYR A:316 , ASN A:319 , LYS A:379 , HOH A:1574BINDING SITE FOR RESIDUE NAG A 1006
07AC7SOFTWAREASP A:433 , GLN A:596 , LEU A:624 , ASN A:625 , NAG A:1008 , HOH A:1558 , HOH A:1699 , HOH A:1767 , HOH A:1962BINDING SITE FOR RESIDUE NAG A 1007
08AC8SOFTWARENAG A:1007 , HOH A:1396 , HOH A:1699BINDING SITE FOR RESIDUE NAG A 1008
09AC9SOFTWAREGLU A:579 , THR A:677 , LEU A:678 , ASN A:681 , HOH A:1119 , HOH A:1541 , HOH A:2035BINDING SITE FOR RESIDUE NAG A 1009
10BC1SOFTWAREGLN A:498 , SER A:502 , GLU A:523 , ALA A:524 , ASN A:527 , GLU A:781BINDING SITE FOR RESIDUE NAG A 1010
11BC2SOFTWAREASN A:784 , ASN A:818BINDING SITE FOR RESIDUE NAG A 1011
12BC3SOFTWAREGLN A:598 , ASN A:735 , ASN A:738BINDING SITE FOR RESIDUE NAG A 1012
13BC4SOFTWAREHIS A:388 , HIS A:392 , GLU A:411 , BES A:1014BINDING SITE FOR RESIDUE ZN A 1013
14BC5SOFTWAREGLN A:213 , ALA A:214 , ALA A:351 , ALA A:353 , GLU A:355 , HIS A:388 , GLU A:389 , HIS A:392 , GLU A:411 , SER A:469 , PHE A:472 , TYR A:477 , GLY A:894 , SER A:895 , ZN A:1013 , HOH A:1118 , HOH A:1176 , HOH A:1315 , HOH A:1382 , HOH A:1445 , HOH A:1919BINDING SITE FOR RESIDUE BES A 1014
15BC6SOFTWARELEU A:131 , GLY A:134 , HIS A:135 , ARG A:136 , LYS A:152 , THR A:153 , HOH A:1565 , HOH A:1740 , HOH A:1824 , HOH A:2033BINDING SITE FOR RESIDUE SO4 A 1015
16BC7SOFTWAREARG A:136 , THR A:153 , GLU A:154 , LEU A:155 , HOH A:1824BINDING SITE FOR RESIDUE SO4 A 1016
17BC8SOFTWAREARG A:690 , HOH A:1332BINDING SITE FOR RESIDUE SO4 A 1017
18BC9SOFTWARETYR A:198 , MET A:199 , ARG A:305 , ARG A:855 , HOH A:1783 , HOH A:1972BINDING SITE FOR RESIDUE SO4 A 1018
19CC1SOFTWARESER A:562 , ARG A:606 , HOH A:1705 , HOH A:1936BINDING SITE FOR RESIDUE SO4 A 1019
20CC2SOFTWARESER A:375 , SER A:377 , SER A:794 , LYS A:827 , HOH A:1154 , HOH A:1633 , HOH A:1651 , HOH A:1920BINDING SITE FOR RESIDUE SO4 A 1020
21CC3SOFTWAREARG A:606 , GLN A:645 , ARG A:648 , HOH A:1549BINDING SITE FOR RESIDUE SO4 A 1021
22CC4SOFTWAREASN A:128 , TYR A:129 , ARG A:136 , LEU A:155 , HOH A:1564 , HOH A:1678 , HOH A:1775BINDING SITE FOR RESIDUE SO4 A 1022
23CC5SOFTWARETYR A:715 , LYS A:719 , GLU A:837 , TRP A:839 , HOH A:1234 , HOH A:1412BINDING SITE FOR RESIDUE SO4 A 1023
24CC6SOFTWAREASN A:736 , PRO A:744 , GLU A:745 , HOH A:1182 , HOH A:1629 , HOH A:2032BINDING SITE FOR RESIDUE SO4 A 1024
25CC7SOFTWAREARG A:537 , LYS A:967 , HOH A:1272BINDING SITE FOR RESIDUE ACY A 1025

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:761 -A:768
2A:798 -A:834

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gln A:213 -Ala A:214

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FYR)

(-) 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:903
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh......eeeeeeeeeeee..........eeeeeeeeeeee.....eeeee....ee.......eeeee........eeeeeee....eeeeee........eeeeeeeeeee......eeeeeeeee..eeeeeeeee....hhhhh...........eeeeeeeee...eeee........eee..eeeeeeee.......hhhhh.eeee..eeeeee.....eeeeeehhhhhhh..hhhhhhhhhhhhhhhhhhh.......eeeeeee......ee....eeeee.hhh.......hhhhhhhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeehhhhhhhhhhhhhhhh......hhhhhhhhhhh....eeeeee....eeeeee....................eee.eee..ee...eee...eee.hhhh......eee.hhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh...hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fyr A  65 PDQSKAWNRYRLPNTLKPDSYRVTLRPYLTPNDRGLYVFKGSSTVRFTCKEATDVIIIHSKKLNYTLSQGHRVVLRGVGGSQPPDIDKTELVEPTEYLVVHLKGSLVKDSQYEMDSEFEGELADDLAGFYRSEYMEGNVRKVVATTQMQAADARKSFPCFDEPAMKAEFNITLIHPKDLTALSNMLPKGPSTPLPEDPNWNVTEFHTTPKMSTYLLAFIVSEFDYVEKQASNGVLIRIWARPSAIAAGHGDYALNVTGPILNFFAGHYDTPYPLPKSDQIGLPDFNAGAMENWGLVTYRENSLLFDPLSSSSSNKERVVTVIAHELAHQWFGNLVTIEWWNDLWLNEGFASYVEYLGADYAEPTWNLKDLMVLNDVYRVMAVDALASSHPLSTPASEINTPAQISELFDAISYSKGASVLRMLSSFLSEDVFKQGLASYLHTFAYQNTIYLNLWDHLQEAVNNRSIQLPTTVRDIMNRWTLQMGFPVITVDTSTGTLSQEHFLLDPDSNVTRPSEFNYVWIVPITSIRDGRQQQDYWLIDVRAQNDLFSTSGNEWVLLNLNVTGYYRVNYDEENWRKIQTQLQRDHSAIPVINRAQIINDAFNLASAHKVPVTLALNNTLFLIEERQYMPWEAALSSLSYFKLMFDRSEVYGPMKNYLKKQVTPLFIHFRNNTNNWREIPENLMDQYSEVNAISTACSNGVPECEEMVSGLFKQWMENPNNNPIHPNLRSTVYCNAIAQGGEEEWDFAWEQFRNATLVNEADKLRAALACSKELWILNRYLSYTLNPDLIRKQDATSTIISITNNVIGQGLVWDFVQSNWKKLFNDYGGGSFSFSNLIQAVTRRFSTEYELQQLEQFKKDNEETGFGSGTRALEQALEKTKANIKWVKENKEVVLQWFTENSK 967
                                    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964
   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  (0, 0)

(no "SCOP Domain" information available for 4FYR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 32)

Asymmetric Unit(hide GO term definitions)

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  4fyr
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  3.4.11.2
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 Related Entries

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

UniProtKB/Swiss-Prot
        AMPN_HUMAN | P15144: 4fyq 4fys 4fyt 5lhd

(-) Related Entries Specified in the PDB File

4fyq 4fys 4fyt