1N51 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   AMINOPEPTIDASE P IN COMPLEX WITH THE INHIBITOR APSTATIN

Authors :   S. C. Graham, M. J. Maher, M. H. Lee, W. H. Simmons, H. C. Freeman, J. M. Gus

Date :   03 Nov 02 (Deposition) - 16 Dec 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (4x)
Biol. Unit 2: A,B  (2x)
Biol. Unit 3: A  (4x)

Keywords :   Aminopeptidase, Proline Specific, Manganese Enzyme, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. C. Graham, M. J. Maher, W. H. Simmons, H. C. Freeman, J. M. Guss
Structure Of Escherichia Coli Aminopeptidase P In Complex With The Inhibitor Apstatin.
Acta Crystallogr. , Sect. D V. 60 1770 2004
PubMed-ID: 15388923 | Reference-DOI: 10.1107/S0907444904018724
(for further references see the PDB file header)

Molecule 1 - XAA-PRO AMINOPEPTIDASE
	Chains	:	A
	EC Number	:	3.4.11.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PPL670
	Expression System Strain	:	AN1459
	Expression System Taxid	:	562
	Expression System Vector	:	PPL450
	Expression System Vector Type	:	PLASMID
	Gene	:	PEPP
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	AMINOPEPTIDASE P

Molecule 2 - APSTATIN
	Chains	:	B
	Engineered	:	YES
	Synthetic	:	YES

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (4x)	:	A	B
Biological Unit 2 (2x)	:	A	B
Biological Unit 3 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	01B	1	Mod. Amino Acid	(2S,3R)-3-AMINO-2-HYDROXY-4-PHENYLBUTANOIC ACID
2	MN	3	Ligand/Ion	MANGANESE (II) ION
3	NH2	1	Mod. Amino Acid	AMINO GROUP

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	01B	4	Mod. Amino Acid	(2S,3R)-3-AMINO-2-HYDROXY-4-PHENYLBUTANOIC ACID
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	NH2	4	Mod. Amino Acid	AMINO GROUP

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	01B	2	Mod. Amino Acid	(2S,3R)-3-AMINO-2-HYDROXY-4-PHENYLBUTANOIC ACID
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	NH2	2	Mod. Amino Acid	AMINO GROUP

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	01B	-1	Mod. Amino Acid	(2S,3R)-3-AMINO-2-HYDROXY-4-PHENYLBUTANOIC ACID
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	NH2	-1	Mod. Amino Acid	AMINO GROUP

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:271 , HIS A:354 , THR A:381 , GLU A:383 , GLU A:406 , MN A:2002 , 01B B:1	BINDING SITE FOR RESIDUE MN A 2001
2	AC2	SOFTWARE	TYR A:229 , ASP A:260 , ASP A:271 , THR A:273 , GLU A:406 , MN A:2001 , 01B B:1	BINDING SITE FOR RESIDUE MN A 2002
3	AC3	SOFTWARE	HOH A:2163 , HOH A:2166 , HOH A:2171 , HOH A:2172 , HOH A:2173 , HOH A:2174	BINDING SITE FOR RESIDUE MN A 2003
4	AC4	SOFTWARE	TRP A:88 , TYR A:229 , HIS A:243 , ASP A:260 , ASP A:271 , HIS A:350 , HIS A:354 , HIS A:361 , GLU A:383 , ARG A:404 , GLU A:406 , MN A:2001 , MN A:2002 , HOH A:2222	BINDING SITE FOR CHAIN B OF APSTATIN

(no "SS Bond" information available for 1N51)

(no "Cis Peptide Bond" information available for 1N51)

(no "SAP(SNP)/Variant" information available for 1N51)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROLINE_PEPTIDASE	PS00491	Aminopeptidase P and proline dipeptidase signature.	AMPP_ECOLI	351-363	1	A:350-362

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROLINE_PEPTIDASE	PS00491	Aminopeptidase P and proline dipeptidase signature.	AMPP_ECOLI	351-363	4	A:350-362

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROLINE_PEPTIDASE	PS00491	Aminopeptidase P and proline dipeptidase signature.	AMPP_ECOLI	351-363	2	A:350-362

Biological Unit 3 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROLINE_PEPTIDASE	PS00491	Aminopeptidase P and proline dipeptidase signature.	AMPP_ECOLI	351-363	4	A:350-362

(no "Exon" information available for 1N51)

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:440
 aligned with AMPP_ECOLI | P15034 from UniProtKB/Swiss-Prot  Length:441

    Alignment length:440
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441
           AMPP_ECOLI     2 SEISRQEFQRRRQALVEQMQPGSAALIFAAPEVTRSADSEYPYRQNSDFWYFTGFNEPEAVLVLIKSDDTHNHSVLFNRVRDLTAEIWFGRRLGQDAAPEKLGVDRALAFSEINQQLYQLLNGLDVVYHAQGEYAYADVIVNSALEKLRKGSRQNLTAPATMIDWRPVVHEMRLFKSPEEIAVLRRAGEITAMAHTRAMEKCRPGMFEYHLEGEIHHEFNRHGARYPSYNTIVGSGENGCILHYTENECEMRDGDLVLIDAGCEYKGYAGDITRTFPVNGKFTQAQREIYDIVLESLETSLRLYRPGTSILEVTGEVVRIMVSGLVKLGILKGDVDELIAQNAHRPFFMHGLSHWLGLDVHDVGVYGQDRSRILEPGMVLTVEPGLYIAPDAEVPEQYRGIGIRIEDDIVITETGNENLTASVVKKPEEIEALMVAARKQ 441
               SCOP domains d1n51a1 A:1-176 Aminopeptidase P                                                                                                                                                d1n51a2 A:177-440 Aminopeptidase P, C-terminal domain                                                                                                                                                                                                                    SCOP domains
               CATH domains 1n51A01 A:1-173 Creatine Amidinohydrolase, subunit A, domain 1                                                                                                               1n51A02 A:174-439 Creatinase/methionine aminopeptidase superfamily                                                                                                                                                                                                        - CATH domains
               Pfam domains --AMP_N-1n51A01 A:3-138                                                                                                                   -------------------------------------------Peptidase_M24-1n51A02 A:182-413                                                                                                                                                                                                         --------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh...eeeeee.....eee..ee.....hhhhhhhhh......eeeeeeee..eeeeeeee...hhhhhhhhh..hhhhhhhhhhh..eeee..hhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh...ee....eeee.hhhhh..............eeeeee.eee..ee..eeeeee.....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.........................hhhhh.......eeee..eeee......hhhhh.eeee..eeeee....eee.......hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PROLINE_PEPTI------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n51 A   1 SEISRQEFQRRRQALVEQMQPGSAALIFAAPEVTRSADSEYPYRQNSDFWYFTGFNEPEAVLVLIKSDDTHNHSVLFNRVRDLTAEIWFGRRLGQDAAPEKLGVDRALAFSEINQQLYQLLNGLDVVYHAQGEYAYADVIVNSALEKLRKGSRQNLTAPATMIDWRPVVHEMRLFKSPEEIAVLRRAGEITAMAHTRAMEKCRPGMFEYHLEGEIHHEFNRHGARYPSYNTIVGSGENGCILHYTENECEMRDGDLVLIDAGCEYKGYAGDITRTFPVNGKFTQAQREIYDIVLESLETSLRLYRPGTSILEVTGEVVRIMVSGLVKLGILKGDVDELIAQNAHRPFFMHGLSHWLGLDVHDVGVYGQDRSRILEPGMVLTVEPGLYIAPDAEVPEQYRGIGIRIEDDIVITETGNENLTASVVKKPEEIEALMVAARKQ 440
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440

Chain B from PDB  Type:PROTEIN  Length:5
                                     
               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
                 1n51 B   1 xPPAx   5
                            |   |
                            1-01B
                                5-NH2

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 '\|'

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: AMP_N-like (22)

Family: AMP_N (11)

Escherichia coli (strain K12) (10)

AMP_N-1n51A01

A:3-138

Clan: no clan defined [family: Peptidase_M24] (23)

Family: Peptidase_M24 (23)

Escherichia coli (strain K12) (10)

Peptidase_M24-1n51A02

A:182-413

Asymmetric Unit(hide GO term definitions)

Chain A (AMPP_ECOLI | P15034)

molecular function
	GO:0004177	aminopeptidase activity	Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008235	metalloexopeptidase activity	Catalysis of the hydrolysis of a peptide bond not more than three residues from the N- or C-terminus of a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008237	metallopeptidase activity	Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		01B	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NH2	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1n51)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1n51
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	AMPP_ECOLI \| P15034
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.4.11.9
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	AMPP_ECOLI \| P15034
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

1a16	PROLEU DIPEPTIDE INHIBITOR COMPLEX, TETRAGONAL FORM, HIGH PH
1az9	NATIVE, HEXAGONAL FORM, HIGH PH
1jaw	ACETATE BOUND, TETRAGONAL FORM, LOW PH
1m35	NATIVE, ORTHORHOMBIC FORM, HIGH PH

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (2, 2)

Pfam Domains (2, 2)

Gene Ontology (12, 12)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File