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(-) Description

Title :  CRYSTAL STRUCTURE OF PORCINE AMINOPEPTIDASE-N COMPLEXED WITH POLY-ALANINE
 
Authors :  L. Chen, Y. L. Lin, G. Peng, F. Li
Date :  22 Oct 13  (Deposition) - 04 Dec 13  (Release) - 04 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
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 Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    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 - POLY A PEPTIDE
    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  (3, 27)

Asymmetric/Biological Unit (3, 27)
No.NameCountTypeFull Name
1NAG15Ligand/IonN-ACETYL-D-GLUCOSAMINE
2SO411Ligand/IonSULFATE ION
3ZN1Ligand/IonZINC ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:84 , ARG A:86 , LYS A:100 , GLY A:101 , LYS A:102 , ILE A:233 , HOH A:1551 , HOH A:1688BINDING SITE FOR RESIDUE SO4 A 1019
02AC2SOFTWAREPRO A:318 , ASN A:321 , HIS A:419 , HOH A:1816BINDING SITE FOR RESIDUE SO4 A 1020
03AC3SOFTWAREPHE A:467 , ASP A:468 , TYR A:472 , SO4 A:1024BINDING SITE FOR RESIDUE SO4 A 1021
04AC4SOFTWARETYR A:748 , ASN A:752 , HOH A:1529 , HOH A:1845BINDING SITE FOR RESIDUE SO4 A 1022
05AC5SOFTWAREPHE A:364 , PRO A:366 , SER A:369 , SER A:370 , ILE A:371 , HOH A:1542BINDING SITE FOR RESIDUE SO4 A 1023
06AC6SOFTWARETYR A:411 , ARG A:480 , ASN A:484 , HOH A:1548 , HOH A:1654 , HOH A:1788BINDING SITE FOR RESIDUE SO4 A 1016
07AC7SOFTWAREASP A:468 , SER A:469 , SO4 A:1021 , HOH A:1616BINDING SITE FOR RESIDUE SO4 A 1024
08AC8SOFTWARELYS A:716 , ARG A:720 , GLY A:802 , GLN A:803BINDING SITE FOR RESIDUE SO4 A 1017
09AC9SOFTWAREPRO A:222 , THR A:395 , LEU A:396 , TRP A:398 , TRP A:399 , HOH A:1624BINDING SITE FOR RESIDUE SO4 A 1025
10BC1SOFTWARELEU A:341 , PRO A:342 , ASP A:343 , ARG A:358 , GLU A:359 , ASN A:360 , VAL A:819 , HOH A:1872BINDING SITE FOR RESIDUE SO4 A 1018
11BC2SOFTWAREMET A:194 , GLU A:195 , GLY A:196 , ASN A:302 , HOH A:1701 , HOH A:1782BINDING SITE FOR RESIDUE SO4 A 1026
12BC3SOFTWAREHIS A:383 , HIS A:387 , GLU A:406 , ALA B:1 , ALA B:2 , HOH B:104BINDING SITE FOR RESIDUE ZN A 1027
13BC4SOFTWAREASN A:82 , ILE A:104 , GLU A:172 , LYS A:247 , NAG A:1004 , HOH A:1702BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 82 RESIDUES 1001 TO 1002
14BC5SOFTWAREASN A:124 , GLN A:178 , GLY A:179 , GLU A:180 , HOH A:1563BINDING SITE FOR MONO-SACCHARIDE NAG A1003 BOUND TO ASN A 124
15BC6SOFTWARESER A:80 , ASN A:82 , ARG A:106 , ASN A:229 , THR A:266 , NAG A:1001 , HOH A:1381 , HOH A:1632 , HOH A:1747BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 229 RESIDUES 1004 TO 1005
16BC7SOFTWARELYS A:200 , ASN A:237 , GLU A:281BINDING SITE FOR MONO-SACCHARIDE NAG A1006 BOUND TO ASN A 237
17BC8SOFTWARETYR A:311 , ASN A:314 , LYS A:374BINDING SITE FOR MONO-SACCHARIDE NAG A1007 BOUND TO ASN A 314
18BC9SOFTWARELEU A:108 , CYS A:109 , GLN A:110 , GLY A:168 , ASN A:328 , HOH A:1591BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 328 RESIDUES 1008 TO 1009
19CC1SOFTWAREALA A:223 , PHE A:502 , GLN A:505 , ASN A:506 , HOH A:1338 , HOH A:1385 , HOH A:1503 , HOH A:1610 , HOH A:1653 , HOH A:1769BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 506 RESIDUES 1010 TO 1011
20CC2SOFTWAREASP A:551 , ASN A:556BINDING SITE FOR MONO-SACCHARIDE NAG A1012 BOUND TO ASN A 556
21CC3SOFTWAREASP A:428 , ASN A:622 , HOH A:1188 , HOH A:1579 , HOH A:1863BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 622 RESIDUES 1013 TO 1014
22CC4SOFTWAREASN A:646 , VAL A:649 , HOH A:1487 , HOH A:1629BINDING SITE FOR MONO-SACCHARIDE NAG A1015 BOUND TO ASN A 646
23CC5SOFTWAREGLN A:208 , ALA A:348 , MET A:349 , GLU A:350 , VAL A:380 , HIS A:383 , GLN A:384 , GLU A:406 , SER A:410 , GLU A:413 , TYR A:414 , GLY A:433 , ASP A:434 , ARG A:437 , TYR A:472 , ZN A:1027 , HOH A:1571 , HOH A:1784 , HOH A:1856 , HOH B:101 , HOH B:102 , HOH B:103 , HOH B:104 , HOH B:105BINDING SITE FOR CHAIN B OF POLY A PEPTIDE

(-) 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 4NAQ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NAQ)

(-) 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:901
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               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......hhhhhhhhhhhhhhhhhhh......ee.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.........hhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhh........hhhhhhhhhhh....eeeee.....eeeeee....................eee.eee..ee...eee....eee.hhhh......eee.hhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhhhhh........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhh.....hhhhhhhhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4naq A  64 SKPWNRYRLPTTLLPDSYNVTLRPYLTPNADGLYIFKGKSIVRFLCQEPTDVIIIHSKKLNYTTQGHMVVLRGVGDSQVPEIDRTELVELTEYLVVHLKGSLQPGHMYEMESEFQGELADDLAGFYRSEYMEGNVKKVLATTQMQSTDARKSFPCFDEPAMKATFNITLIHPNNLTALSNMPPKGSSTPLAEDPNWSVTEFETTPVMSTYLLAYIVSEFQSVNETAQNGVLIRIWARPNAIAEGHGMYALNVTGPILNFFANHYNTSYPLPKSDQIALPDFNAGAMENWGLVTYRENALLFDPQSSSISNKERVVTVIAHQLAHQWFGNLVTLAWWNDLWLNEGFASYVEYLGADHAEPTWNLKDLIVPGDVYRVMAVDALASSHPLTTPAEEVNTPAQISEMFDSISYSKGASVIRMLSNFLTEDLFKEGLASYLHAFAYQNTTYLDLWEHLQKAVDAQTSIRLPDTVRAIMDRWTLQMGFPVITVDTKTGNISQKHFLLDSESNVTRSSAFDYLWIVPISSIKNGVMQDHYWLRDVSQAQNDLFKTASDDWVLLNVNVTGYFQVNYDEDNWRMIQHQLQTNLSVIPVINRAQVIYDSFNLATAHMVPVTLALDNTLFLNGEKEYMPWQAALSSLSYFSLMFDRSEVYGPMKKYLRKQVEPLFQHFETLTKNWTERPENLMDQYSEINAISTACSNGLPQCENLAKTLFDQWMSDPENNPIHPNLRSTIYCNAIAQGGQDQWDFAWGQLQQAQLVNEADKLRSALACSNEVWLLNRYLGYTLNPDLIRKQDATSTINSIASNVIGQPLAWDFVQSNWKKLFQDYGGGSFSFSNLIQGVTRRFSSEFELQQLEQFKKNNMDVGFGSGTRALEQALEKTKANIKWVKENKEVVLNWFIEHSS 964
                                    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       503       513       523       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 


Chain B from PDB  Type:PROTEIN  Length:7
                                       
               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
                 4naq B   1 AAAAAAA   7
   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 4NAQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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        AMPN_PIG | P15145: 4f5c 4fke 4fkh 4fkk 4hom 4nz8 4ou3 5lds 5lg6

(-) Related Entries Specified in the PDB File

4fke CRYSTAL STRUCTURE OF PORCINE AMINOPEPTIDASE-N