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(-) Description

Title :  HUMAN AMINOPEPTIDASE N (CD13)
 
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 :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Metalloprotease, Hydrolase (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
    Fragment: UNP RESIDUES 66-967
    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  (5, 24)

Asymmetric Unit (5, 24)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2BMA1Ligand/IonBETA-D-MANNOSE
3NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SO411Ligand/IonSULFATE ION
5ZN1Ligand/IonZINC ION
Biological Unit 1 (4, 46)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2BMA2Ligand/IonBETA-D-MANNOSE
3NAG20Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SO422Ligand/IonSULFATE ION
5ZN-1Ligand/IonZINC ION

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:128 , GLY A:184 , GLU A:185 , HOH A:1500 , HOH A:1584 , HOH A:1617BINDING 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:1632BINDING SITE FOR RESIDUE NAG A 1002
03AC3SOFTWAREARG A:110 , NAG A:1002 , BMA A:1004BINDING SITE FOR RESIDUE NAG A 1003
04AC4SOFTWARENAG A:1003BINDING 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:1254 , HOH A:1597BINDING SITE FOR RESIDUE NAG A 1005
06AC6SOFTWARETYR A:316 , ASN A:319 , HOH A:1484BINDING SITE FOR RESIDUE NAG A 1006
07AC7SOFTWAREASP A:433 , GLN A:596 , LEU A:624 , ASN A:625 , NAG A:1008 , HOH A:1452 , HOH A:1535 , HOH A:1658BINDING SITE FOR RESIDUE NAG A 1007
08AC8SOFTWARENAG A:1007BINDING SITE FOR RESIDUE NAG A 1008
09AC9SOFTWAREGLU A:579 , THR A:677 , LEU A:678 , ASN A:681 , HOH A:1109 , HOH A:1763BINDING SITE FOR RESIDUE NAG A 1009
10BC1SOFTWAREGLN A:498 , SER A:502 , ALA A:524 , ASN A:527 , GLU A:781BINDING SITE FOR RESIDUE NAG A 1010
11BC2SOFTWAREASN A:784 , ASN A:818 , THR A:820BINDING SITE FOR RESIDUE NAG A 1011
12BC3SOFTWAREHIS A:388 , HIS A:392 , GLU A:411 , ACY A:1024BINDING SITE FOR RESIDUE ZN A 1012
13BC4SOFTWAREGLY A:134 , HIS A:135 , ARG A:136 , LYS A:152 , THR A:153 , HOH A:1489BINDING SITE FOR RESIDUE SO4 A 1013
14BC5SOFTWAREARG A:136 , THR A:153 , GLU A:154 , LEU A:155BINDING SITE FOR RESIDUE SO4 A 1014
15BC6SOFTWAREARG A:690 , HOH A:1246 , HOH A:1328BINDING SITE FOR RESIDUE SO4 A 1015
16BC7SOFTWARESER A:562 , ARG A:606 , HOH A:1154BINDING SITE FOR RESIDUE SO4 A 1016
17BC8SOFTWARESER A:375 , SER A:377 , SER A:794 , LYS A:827 , HOH A:1128 , HOH A:1341 , HOH A:1638 , HOH A:1710BINDING SITE FOR RESIDUE SO4 A 1017
18BC9SOFTWAREARG A:606 , GLN A:645 , ARG A:648BINDING SITE FOR RESIDUE SO4 A 1018
19CC1SOFTWAREASN A:128 , TYR A:129 , ARG A:136 , LEU A:155 , HOH A:1584 , HOH A:1605BINDING SITE FOR RESIDUE SO4 A 1019
20CC2SOFTWARETYR A:715 , LYS A:719 , GLU A:837 , TRP A:839 , HOH A:1184 , HOH A:1672 , HOH A:1701BINDING SITE FOR RESIDUE SO4 A 1020
21CC3SOFTWARETYR A:198 , MET A:199 , ARG A:305 , ARG A:855 , HOH A:1612 , HOH A:1722BINDING SITE FOR RESIDUE SO4 A 1021
22CC4SOFTWARESER A:651 , ARG A:658 , GLN A:691BINDING SITE FOR RESIDUE SO4 A 1022
23CC5SOFTWAREARG A:537 , LYS A:967BINDING SITE FOR RESIDUE SO4 A 1023
24CC6SOFTWAREALA A:353 , GLU A:355 , HIS A:388 , GLU A:389 , HIS A:392 , GLU A:411 , TYR A:477 , ZN A:1012BINDING SITE FOR RESIDUE ACY A 1024

(-) 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 4FYQ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FYQ)

(-) 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:892
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh......eeeeeeeeeeee..........eeeeeeeeeeee.....eeeee....ee.......eeeee........eeeeeee....eeeeee.......eeeeeeeeeeee......eeeeeeeee..eeeeeeeee....hhhhh...........eeeeeeeee...eeee........ee......eeeee.......hhhhh.eeee..eeeeee.....eeeeeehhhhhhh..hhhhhhhhhhhhhhhhhhh.......eeeeeee......ee....eeeeehhhhh......hhhhhhhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.........hhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeehhhhhhhhhhhhhhhh......hhhhhhhhhhh....eeeeee....eeeeee....................eee.eee..ee...eee...eee.hhhh......eee.hhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fyq A  68 SKAWNRYRLPNTLKPDSYRVTLRPYLTPNDRGLYVFKGSSTVRFTCKEATDVIIIHSKKLNYTLSQGHRVVLRGVGGSQPPDIDKTELVEPTEYLVVHLKGSLVKDSQYEMDSEFEGELADDLAGFYRSEYMEGNVRKVVATTQMQAADARKSFPCFDEPAMKAEFNITLIHPKDLTALSNMLPKGPSTPLPEDPNWNVTEFHTTPKMSTYLLAFIVSEFDYVEKQASNGVLIRIWARPSAIAAGHGDYALNVTGPILNFFAGHYDTPYPLPKSDQIGLPDFNAGAMENWGLVTYRENSLLFDPLSSSSSNKERVVTVIAHELAHQWFGNLVTIEWWNDLWLNEGFASYVEYLGADYAEPTWNLKDLMVLNDVYRVMAVDALASSHPLSTPASEINTPAQISELFDAISYSKGASVLRMLSSFLSEDVFKQGLASYLHTFAYQNTIYLNLWDHLQEAVNNRSIQLPTTVRDIMNRWTLQMGFPVITVDTSTGTLSQEHFLLDPDSNVTRPSEFNYVWIVPITSIRDGRQQQDYWLIDVRAQNDLFSTSGNEWVLLNLNVTGYYRVNYDEENWRKIQTQLQRDHSAIPVINRAQIINDAFNLASAHKVPVTLALNNTLFLIEERQYMPWEAALSSLSYFKLMFDRSEVYGPMKNYLKKQVTPLFIHFRNNTNNWREIPENLMDQYSEVNAISTACSNGVPECEEMVSGLFKQWMENPNNNPIHPNLRSTVYCNAIAQGGEEEWDFAWEQFRNATLVNEADKLRAALACSKELWILNRYLSYTLNPDLIRKQDATSTIISITNNVIGQGLVWDFVQSNWKKLFNDSNLIQAVTRRFSTEYELQQLEQFKKDNEETGFGSGTRALEQALEKTKANIKWVKENKEVVLQWFTENSK 967
                                    77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       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  ||   905       915       925       935       945       955       965  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                890|                                                                    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 899
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 32)

Asymmetric Unit(hide GO term definitions)

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  3.4.11.2
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 Related Entries

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

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        AMPN_HUMAN | P15144: 4fyr 4fys 4fyt 5lhd

(-) Related Entries Specified in the PDB File

4fyr 4fys 4fyt