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(-) Description

Title :  HUMAN AMINOPEPTIDASE N (CD13) IN COMPLEX WITH AMASTATIN
 
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 :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (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
    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
 
Molecule 2 - AMASTATIN
    Chains: B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 25)

Asymmetric Unit (4, 25)
No.NameCountTypeFull Name
1L2O1Mod. Amino Acid(2S,3R)-3-AMINO-2-HYDROXY-5-METHYLHEXANOIC ACID
2NAG11Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SO412Ligand/IonSULFATE ION
4ZN1Ligand/IonZINC ION
Biological Unit 1 (3, 48)
No.NameCountTypeFull Name
1L2O2Mod. Amino Acid(2S,3R)-3-AMINO-2-HYDROXY-5-METHYLHEXANOIC ACID
2NAG22Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SO424Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:388 , HIS A:392 , GLU A:411 , L2O B:1BINDING SITE FOR RESIDUE ZN A 1012
02AC2SOFTWARELEU A:131 , GLY A:134 , HIS A:135 , ARG A:136 , LYS A:152 , THR A:153 , HOH A:1708BINDING SITE FOR RESIDUE SO4 A 1013
03AC3SOFTWAREARG A:136 , THR A:153 , GLU A:154 , LEU A:155BINDING SITE FOR RESIDUE SO4 A 1014
04AC4SOFTWAREARG A:690 , HOH A:1278BINDING SITE FOR RESIDUE SO4 A 1015
05AC5SOFTWARESER A:562 , ARG A:606 , HOH A:1647BINDING SITE FOR RESIDUE SO4 A 1016
06AC6SOFTWARESER A:375 , SER A:377 , SER A:794 , LYS A:827 , HOH A:1111 , HOH A:1256 , HOH A:1540BINDING SITE FOR RESIDUE SO4 A 1017
07AC7SOFTWAREARG A:606 , GLN A:645 , ARG A:648 , HOH A:1411 , HOH A:1578BINDING SITE FOR RESIDUE SO4 A 1018
08AC8SOFTWAREASN A:128 , TYR A:129 , ARG A:136 , LEU A:155 , HOH A:1515 , HOH A:1707BINDING SITE FOR RESIDUE SO4 A 1019
09AC9SOFTWARETYR A:715 , LYS A:719 , GLU A:837 , TRP A:839 , HOH A:1173 , HOH A:1317 , HOH A:1518BINDING SITE FOR RESIDUE SO4 A 1020
10BC1SOFTWAREASN A:736 , PRO A:744 , GLU A:745 , HOH A:1168 , HOH A:1574BINDING SITE FOR RESIDUE SO4 A 1021
11BC2SOFTWAREARG A:537 , LYS A:967 , HOH A:1177BINDING SITE FOR RESIDUE SO4 A 1022
12BC3SOFTWARESER A:651 , ARG A:658 , GLN A:691BINDING SITE FOR RESIDUE SO4 A 1023
13BC4SOFTWARETYR A:198 , MET A:199 , ARG A:305 , ARG A:855BINDING SITE FOR RESIDUE SO4 A 1024
14BC5SOFTWAREASN A:128 , GLY A:184 , GLU A:185 , HOH A:1590 , HOH A:1705BINDING SITE FOR MONO-SACCHARIDE NAG A1001 BOUND TO ASN A 128
15BC6SOFTWARESER A:84 , TYR A:85 , ARG A:86 , ARG A:110 , ASN A:234 , THR A:271BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 234 RESIDUES 1002 TO 1003
16BC7SOFTWAREHIS A:239 , LYS A:241 , LEU A:243 , SER A:255 , PRO A:257 , ASN A:265 , HOH A:1364BINDING SITE FOR MONO-SACCHARIDE NAG A1004 BOUND TO ASN A 265
17BC8SOFTWARETYR A:316 , ASN A:319BINDING SITE FOR MONO-SACCHARIDE NAG A1005 BOUND TO ASN A 319
18BC9SOFTWAREGLN A:498 , SER A:502 , GLU A:523 , ASN A:527 , GLU A:781BINDING SITE FOR MONO-SACCHARIDE NAG A1010 BOUND TO ASN A 527
19CC1SOFTWAREASP A:433 , GLN A:596 , LEU A:624 , ASN A:625 , HOH A:1509 , HOH A:1552 , HOH A:1656BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 625 RESIDUES 1006 TO 1007
20CC2SOFTWAREGLU A:579 , THR A:677 , LEU A:678 , ASN A:681 , HOH A:1117 , HOH A:1294BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 681 RESIDUES 1008 TO 1009
21CC3SOFTWAREASN A:818BINDING SITE FOR MONO-SACCHARIDE NAG A1011 BOUND TO ASN A 818
22CC4SOFTWAREGLN A:211 , GLN A:213 , ALA A:351 , GLY A:352 , ALA A:353 , GLU A:355 , ARG A:363 , ARG A:381 , HIS A:388 , GLU A:389 , HIS A:392 , GLU A:411 , TYR A:477 , PHE A:896 , ZN A:1012 , HOH B:101 , HOH B:102BINDING SITE FOR CHAIN B OF AMASTATIN

(-) 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 4FYT)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FYT)

(-) 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....eeeeehhhhh......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.hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fyt 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   


Chain B from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 4fyt B   1 xVVD   4
                            |   
                            1-L2O
   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 4FYT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 32)

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  4fyt
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  3.4.11.2
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 Related Entries

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

(-) Related Entries Specified in the PDB File

4fyq 4fyr 4fys