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(-) Description

Title :  CRYSTAL STRUCTURE OF PORCINE AMINOPEPTIDASE-N COMPLEXED WITH SUBSTANCE P
 
Authors :  L. Chen, Y. L. Lin, G. Peng, F. Li
Date :  22 Oct 12  (Deposition) - 31 Oct 12  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Zinc Aminopeptidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Chen, Y. L. Lin, G. Peng, F. Li
Structural Basis For Multifunctional Roles Of Mammalian Aminopeptidase N.
Proc. Natl. Acad. Sci. Usa V. 109 17966 2012
PubMed-ID: 23071329  |  Reference-DOI: 10.1073/PNAS.1210123109

(-) Compounds

Molecule 1 - AMINOPEPTIDASE N
    Chains: A
    EC Number: 3.4.11.2
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFASTBAC
    Expression System Strain: SF9
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 62-963
    Gene: ANPEP
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Synonym: AP-N, PAPN, ALANYL AMINOPEPTIDASE, AMINOPEPTIDASE M, AP-M, MICROSOMAL AMINOPEPTIDASE, GP130
 
Molecule 2 - SUBSTANCE P
    Chains: B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 24)

Asymmetric/Biological Unit (2, 24)
No.NameCountTypeFull Name
1NAG23Ligand/IonN-ACETYL-D-GLUCOSAMINE
2ZN1Ligand/IonZINC ION

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:82 , ILE A:104 , GLU A:172 , NAG A:1002 , NAG A:1007 , HOH A:1551 , HOH A:1600 , HOH A:1706 , HOH A:1839 , HOH A:1845 , HOH A:2005 , HOH A:2132 , HOH A:2148BINDING SITE FOR RESIDUE NAG A 1001
02AC2SOFTWARENAG A:1001 , NAG A:1003 , NAG A:1007 , HOH A:1706 , HOH A:1839 , HOH A:2291 , HOH A:2385BINDING SITE FOR RESIDUE NAG A 1002
03AC3SOFTWARENAG A:1002 , HOH A:2191 , HOH A:2214BINDING SITE FOR RESIDUE NAG A 1003
04AC4SOFTWAREASN A:124 , GLN A:178 , GLY A:179 , GLU A:180 , NAG A:1005 , HOH A:1436 , HOH A:1887 , HOH A:1986 , HOH A:2356BINDING SITE FOR RESIDUE NAG A 1004
05AC5SOFTWARENAG A:1004 , NAG A:1006 , HOH A:2020 , HOH A:2387 , HOH A:2518BINDING SITE FOR RESIDUE NAG A 1005
06AC6SOFTWAREASP A:94 , NAG A:1005 , HOH A:2512BINDING SITE FOR RESIDUE NAG A 1006
07AC7SOFTWARESER A:80 , ASN A:82 , ARG A:106 , ASN A:229 , THR A:266 , NAG A:1001 , NAG A:1002 , NAG A:1008 , HOH A:1471BINDING SITE FOR RESIDUE NAG A 1007
08AC8SOFTWARENAG A:1007 , HOH A:1147 , HOH A:1683 , HOH A:2248 , HOH A:2502BINDING SITE FOR RESIDUE NAG A 1008
09AC9SOFTWARELYS A:200 , ASN A:237 , GLU A:281 , NAG A:1010 , HOH A:1962BINDING SITE FOR RESIDUE NAG A 1009
10BC1SOFTWARENAG A:1009 , HOH A:1878 , HOH A:2421BINDING SITE FOR RESIDUE NAG A 1010
11BC2SOFTWARETYR A:311 , ASN A:314 , LYS A:374 , NAG A:1012 , HOH A:2018 , HOH A:2217BINDING SITE FOR RESIDUE NAG A 1011
12BC3SOFTWARELEU A:153 , NAG A:1011 , NAG A:1013 , HOH A:1511 , HOH A:1781 , HOH A:2192 , HOH A:2399BINDING SITE FOR RESIDUE NAG A 1012
13BC4SOFTWARENAG A:1012 , HOH A:1657 , HOH A:1735 , HOH A:2189 , HOH A:2507BINDING SITE FOR RESIDUE NAG A 1013
14BC5SOFTWAREASN A:328 , NAG A:1015 , HOH A:1672 , HOH A:1967 , HOH A:2249 , HOH A:2496BINDING SITE FOR RESIDUE NAG A 1014
15BC6SOFTWARECYS A:109 , GLN A:110 , GLY A:168 , NAG A:1014 , HOH A:2023 , HOH A:2031 , HOH A:2259 , HOH A:2310 , HOH A:2311 , HOH A:2343BINDING SITE FOR RESIDUE NAG A 1015
16BC7SOFTWAREALA A:223 , PHE A:502 , GLN A:505 , ASN A:506 , NAG A:1017 , HOH A:1164 , HOH A:1413 , HOH A:1479 , HOH A:1908 , HOH A:2033BINDING SITE FOR RESIDUE NAG A 1016
17BC8SOFTWAREGLN A:505 , NAG A:1016 , HOH A:1666 , HOH A:2264BINDING SITE FOR RESIDUE NAG A 1017
18BC9SOFTWAREASP A:551 , ASN A:556 , GLN A:603 , NAG A:1019BINDING SITE FOR RESIDUE NAG A 1018
19CC1SOFTWARENAG A:1018 , HOH A:2379 , HOH A:2521BINDING SITE FOR RESIDUE NAG A 1019
20CC2SOFTWAREGLU A:567 , ASN A:569 , HOH A:2292 , HOH A:2375 , HOH A:2429 , HOH A:2432 , HOH A:2520BINDING SITE FOR RESIDUE NAG A 1020
21CC3SOFTWAREASP A:428 , ASN A:622 , NAG A:1022 , HOH A:1148 , HOH A:1218 , HOH A:1778 , HOH A:2242BINDING SITE FOR RESIDUE NAG A 1021
22CC4SOFTWAREASN A:425 , NAG A:1021 , HOH A:2069 , HOH A:2196 , HOH A:2242BINDING SITE FOR RESIDUE NAG A 1022
23CC5SOFTWAREASN A:646 , HOH A:1893 , HOH A:2276BINDING SITE FOR RESIDUE NAG A 1023
24CC6SOFTWAREHIS A:383 , HIS A:387 , GLU A:406 , HOH A:1506 , ARG B:1BINDING SITE FOR RESIDUE ZN A 1024

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:758 -A:765
2A:795 -A:831

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:208 -Ser A:209

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HOM)

(-) Sequences/Alignments

Asymmetric/Biological 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:902
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh......eeeeeeeeeeee..........eeeeeeeeeeee...eeeeeee....ee.......eeee........eeeeeee....eeeeeeeeee....eeeeeeeeeee......eeeeeeeee..eeeeeeeee....hhhhh...........eeeeeeeee...eeee........ee......eeeee.......hhhhh.eeee..eeeeee.....eeeeeehhhhhhh..hhhhhhhhhhhhhhhhhhh.......eeeeeee......ee....eeeeehhhhh......hhhhhhhhhhhhhhhhhh.......ee.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.........hhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhh........hhhhhhhhhhh....eeeee.....eeeeee....................eee.eee..ee...eee....eee.hhhh......eee.hhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhh........hhhhhhhhhhhhhhh.hhhhhhhhhhhhh.............hhhhhhhhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hom A  63 QSKPWNRYRLPTTLLPDSYNVTLRPYLTPNADGLYIFKGKSIVRFLCQEPTDVIIIHSKKLNYTTQGHMVVLRGVGDSQVPEIDRTELVELTEYLVVHLKGSLQPGHMYEMESEFQGELADDLAGFYRSEYMEGNVKKVLATTQMQSTDARKSFPCFDEPAMKATFNITLIHPNNLTALSNMPPKGSSTPLAEDPNWSVTEFETTPVMSTYLLAYIVSEFQSVNETAQNGVLIRIWARPNAIAEGHGMYALNVTGPILNFFANHYNTSYPLPKSDQIALPDFNAGAMENWGLVTYRENALLFDPQSSSISNKERVVTVIAHELAHQWFGNLVTLAWWNDLWLNEGFASYVEYLGADHAEPTWNLKDLIVPGDVYRVMAVDALASSHPLTTPAEEVNTPAQISEMFDSISYSKGASVIRMLSNFLTEDLFKEGLASYLHAFAYQNTTYLDLWEHLQKAVDAQTSIRLPDTVRAIMDRWTLQMGFPVITVDTKTGNISQKHFLLDSESNVTRSSAFDYLWIVPISSIKNGVMQDHYWLRDVSQAQNDLFKTASDDWVLLNVNVTGYFQVNYDEDNWRMIQHQLQTNLSVIPVINRAQVIYDSFNLATAHMVPVTLALDNTLFLNGEKEYMPWQAALSSLSYFSLMFDRSEVYGPMKKYLRKQVEPLFQHFETLTKNWTERPENLMDQYSEINAISTACSNGLPQCENLAKTLFDQWMSDPENNPIHPNLRSTIYCNAIAQGGQDQWDFAWGQLQQAQLVNEADKLRSALACSNEVWLLNRYLGYTLNPDLIRKQDATSTINSIASNVIGQPLAWDFVQSNWKKLFQDYGGGSFSFSNLIQGVTRRFSSEFELQQLEQFKKNNMDVGFGSGTRALEQALEKTKANIKWVKENKEVVLNWFIEHSS 964
                                    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:11
                                           
               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
                 4hom B   1 RPKPQQFFGLM  11
                                    10
   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 4HOM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (62, 63)

Asymmetric/Biological Unit(hide GO term definitions)

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  4hom
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 Related Entries

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

UniProtKB/Swiss-Prot
        AMPN_PIG | P15145: 4f5c 4fke 4fkh 4fkk 4naq 4nz8 4ou3 5lds 5lg6
        TKN1_HUMAN | P20366: 2b19 2ks9 2ksa 2ksb

(-) Related Entries Specified in the PDB File

4fke CRYSTAL STRUCTURE OF PORCINE AMINOPEPTIDASE-N
4fkh CRYSTAL STRUCTURE OF PORCINE AMINOPEPTIDASE-N COMPLEXED WITH ALANINE
4fkk CRYSTAL STRUCTURE OF PORCINE AMINOPEPTIDASE-N COMPLEXED WITH BESTATIN
4hol CRYSTAL STRUCTURE OF PORCINE AMINOPEPTIDASE-N COMPLEXED WITH POLY-ALANINE