1IYK - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF CANDIDA ALBICANS N-MYRISTOYLTRANSFERASE WITH MYRISTOYL-COA AND PEPTIDIC INHIBITOR

Authors :   S. Sogabe, T. A. Fukami, K. Morikami, Y. Shiratori, Y. Aoki, A. D'Arcy, F. K. Winkler, D. W. Banner, T. Ohtsuka

Date :   29 Aug 02 (Deposition) - 30 Dec 02 (Release) - 09 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Sogabe, M. Masubuchi, K. Sakata, T. A. Fukami, K. Morikami, Y. Shiratori, H. Ebiike, K. Kawasaki, Y. Aoki, N. Shimma, A. D'Arcy, F. K. Winkler, D. W. Banner, T. Ohtsuka
Crystal Structures Of Candida Albicans N-Myristoyltransferase With Two Distinct Inhibitors
Chem. Biol. V. 9 1119 2002
PubMed-ID: 12401496 | Reference-DOI: 10.1016/S1074-5521(02)00240-5

Molecule 1
	Chains	:	A, B
	EC Number	:	2.3.1.97
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKF19
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 60-451
	Organism Scientific	:	CANDIDA ALBICANS
	Organism Taxid	:	5476
	Synonym	:	GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	MIM	2	Ligand/Ion	[CYCLOHEXYLETHYL]-[[[[4-[2-METHYL-1-IMIDAZOLYL-BUTYL]PHENYL]ACETYL]-SERYL]-LYSINYL]-AMINE
2	MYA	2	Ligand/Ion	TETRADECANOYL-COA

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	MIM	1	Ligand/Ion	[CYCLOHEXYLETHYL]-[[[[4-[2-METHYL-1-IMIDAZOLYL-BUTYL]PHENYL]ACETYL]-SERYL]-LYSINYL]-AMINE
2	MYA	1	Ligand/Ion	TETRADECANOYL-COA

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	MIM	1	Ligand/Ion	[CYCLOHEXYLETHYL]-[[[[4-[2-METHYL-1-IMIDAZOLYL-BUTYL]PHENYL]ACETYL]-SERYL]-LYSINYL]-AMINE
2	MYA	1	Ligand/Ion	TETRADECANOYL-COA

Biological Unit 3 (2, 4)

No.	Name	Count	Type	Full Name
1	MIM	2	Ligand/Ion	[CYCLOHEXYLETHYL]-[[[[4-[2-METHYL-1-IMIDAZOLYL-BUTYL]PHENYL]ACETYL]-SERYL]-LYSINYL]-AMINE
2	MYA	2	Ligand/Ion	TETRADECANOYL-COA

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:107 , VAL A:108 , PHE A:176 , LEU A:177 , CYS A:178 , ILE A:179 , ARG A:184 , ASN A:185 , LYS A:186 , ARG A:187 , LEU A:188 , ALA A:189 , PRO A:190 , THR A:197 , TRP A:206 , GLN A:207 , TYR A:210 , THR A:211 , LEU A:216 , PHE A:420 , HOH A:513	BINDING SITE FOR RESIDUE MYA A 501
2	AC2	SOFTWARE	VAL A:108 , GLU A:109 , ASP A:110 , ASP A:112 , PHE A:117 , TYR A:119 , ASN A:175 , THR A:211 , TYR A:225 , HIS A:227 , PHE A:240 , TYR A:256 , GLY A:409 , SER A:410 , GLY A:411 , ASP A:412 , GLY A:413 , LEU A:415 , LEU A:451 , HOH A:507 , HOH A:517 , HOH A:526	BINDING SITE FOR RESIDUE MIM A 502
3	AC3	SOFTWARE	TYR B:107 , VAL B:108 , ILE B:174 , PHE B:176 , LEU B:177 , CYS B:178 , ILE B:179 , ARG B:184 , ASN B:185 , LYS B:186 , ARG B:187 , LEU B:188 , ALA B:189 , PRO B:190 , THR B:197 , ASN B:201 , TRP B:206 , ALA B:208 , TYR B:210 , THR B:211 , ILE B:215 , LEU B:216 , PHE B:420 , HOH B:1509	BINDING SITE FOR RESIDUE MYA B 1501
4	AC4	SOFTWARE	VAL B:108 , GLU B:109 , ASP B:110 , ILE B:111 , ASP B:112 , PHE B:115 , PHE B:117 , ASN B:175 , THR B:211 , TYR B:225 , HIS B:227 , PHE B:240 , TYR B:256 , PHE B:339 , GLY B:409 , SER B:410 , GLY B:411 , ASP B:412 , GLY B:413 , LEU B:415 , LEU B:451 , HOH B:1525 , HOH B:1532	BINDING SITE FOR RESIDUE MIM B 1502

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

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

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NMT_1	PS00975	Myristoyl-CoA:protein N-myristoyltransferase signature 1.	NMT_CANAL	173-181	2	A:173-181 B:173-181
2	NMT_2	PS00976	Myristoyl-CoA:protein N-myristoyltransferase signature 2.	NMT_CANAL	407-413	2	A:407-413 B:407-413

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NMT_1	PS00975	Myristoyl-CoA:protein N-myristoyltransferase signature 1.	NMT_CANAL	173-181	1	A:173-181 -
2	NMT_2	PS00976	Myristoyl-CoA:protein N-myristoyltransferase signature 2.	NMT_CANAL	407-413	1	A:407-413 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NMT_1	PS00975	Myristoyl-CoA:protein N-myristoyltransferase signature 1.	NMT_CANAL	173-181	1	- B:173-181
2	NMT_2	PS00976	Myristoyl-CoA:protein N-myristoyltransferase signature 2.	NMT_CANAL	407-413	1	- B:407-413

Biological Unit 3 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NMT_1	PS00975	Myristoyl-CoA:protein N-myristoyltransferase signature 1.	NMT_CANAL	173-181	2	A:173-181 B:173-181
2	NMT_2	PS00976	Myristoyl-CoA:protein N-myristoyltransferase signature 2.	NMT_CANAL	407-413	2	A:407-413 B:407-413

(no "Exon" information available for 1IYK)

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:392
 aligned with NMT_CANAL | P30418 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:392
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449  
            NMT_CANAL    60 EGPIDKLKTPEDVPNDPLPLISDFEWSTLDIDDNLQLDELYKLLYDNYVEDIDATFRFKYSHEFFQWALKPPGWRKDWHVGVRVKSTGKLVAFIAATPVTFKLNKSNKVIDSVEINFLCIHKKLRNKRLAPVLIKEITRRVNKQNIWQALYTGGSILPTPLTTCRYQHRPINWSKLHDVGFSHLPPNQTKSSMVASYTLPNNPKLKGLRPMTGKDVSTVLSLLYKYQERFDIVQLFTEEEFKHWMLGHDENSDSNVVKSYVVEDENGVITDYFSYYLLPFTVLDNAQHDELGIAYLFYYASDSFEKPNYKKRLNELITDALITSKKFGVDVFNCLTCQDNTYFLKDCKFGSGDGFLNYYLFNYRTFPMDGGIDKKTKEVVEDQTSGIGVVLL 451
               SCOP domains d1iyka1 A:60-224 N-myristoyl transferase, NMT                                                                                                                        d1iyka2 A:225-451 N-myristoyl transferase, NMT                                                                                                                                                                                      SCOP domains
               CATH domains 1iykA01 A:60-206  [code=3.40.630.30, no name defined]                                                                                              1iykA02 A:207-451  [code=3.40.630.30, no name defined]                                                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh..........eeeee....hhhhhhhhhhhhhhhh.......eee..hhhhhhhhhh....hhh.eeeeee.....eeeeeeeeeeeeee....eeeeeeeeeeeee.hhhh...hhhhhhhhhhhhhhh.....eeeee........eeeeeeeee.hhhhhhhh.........hhhhhhhhhh.........eee.hhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhh.........eeeeeee.....eeeeeeeee..eee.......ee.eeeeeeeee......hhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhh......eeeeeeeeeeee.........................ee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------NMT_1    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NMT_2  -------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iyk A  60 EGPIDKLKTPEDVPNDPLPLISDFEWSTLDIDDNLQLDELYKLLYDNYVEDIDATFRFKYSHEFFQWALKPPGWRKDWHVGVRVKSTGKLVAFIAATPVTFKLNKSNKVIDSVEINFLCIHKKLRNKRLAPVLIKEITRRVNKQNIWQALYTGGSILPTPLTTCRYQHRPINWSKLHDVGFSHLPPNQTKSSMVASYTLPNNPKLKGLRPMTGKDVSTVLSLLYKYQERFDIVQLFTEEEFKHWMLGHDENSDSNVVKSYVVEDENGIITDYFSYYLLPFTVLDNAQHDELGIAYLFYYASDSFEKPNYKKRLNELITDALITSKKFGVDVFNCLTCQDNTYFLKDCKFGSGDGFLNYYLFNYRTFPMDGGIDKKTKEVVEDQTSGIGVVLL 451
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449

Chain B from PDB  Type:PROTEIN  Length:392
 aligned with NMT_CANAL | P30418 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:392
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449  
            NMT_CANAL    60 EGPIDKLKTPEDVPNDPLPLISDFEWSTLDIDDNLQLDELYKLLYDNYVEDIDATFRFKYSHEFFQWALKPPGWRKDWHVGVRVKSTGKLVAFIAATPVTFKLNKSNKVIDSVEINFLCIHKKLRNKRLAPVLIKEITRRVNKQNIWQALYTGGSILPTPLTTCRYQHRPINWSKLHDVGFSHLPPNQTKSSMVASYTLPNNPKLKGLRPMTGKDVSTVLSLLYKYQERFDIVQLFTEEEFKHWMLGHDENSDSNVVKSYVVEDENGVITDYFSYYLLPFTVLDNAQHDELGIAYLFYYASDSFEKPNYKKRLNELITDALITSKKFGVDVFNCLTCQDNTYFLKDCKFGSGDGFLNYYLFNYRTFPMDGGIDKKTKEVVEDQTSGIGVVLL 451
               SCOP domains d1iykb1 B:60-224 N-myristoyl transferase, NMT                                                                                                                        d1iykb2 B:225-451 N-myristoyl transferase, NMT                                                                                                                                                                                      SCOP domains
               CATH domains 1iykB01 B:60-206  [code=3.40.630.30, no name defined]                                                                                              1iykB02 B:207-451  [code=3.40.630.30, no name defined]                                                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh..........eeeee....hhhhhhhhhhhhhhhh.......eee..hhhhhhhhh.....hhh.eeeeee.....eeeeeeeeeeeeee....eeeeeeeeeeeee.hhhh...hhhhhhhhhhhhhhh.....eeeee........eeeeeeeee.hhhhhhhh.........hhhhhhhhhh.........eee....hhhhhhhhhhhhhh...eeee.hhhhhhhhhhh.........eeeeeee.....eeeeeeeee..eee.......ee.eeeeeeeee.hhhh.hhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhh......eeeeeeeeeeee.........................ee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------NMT_1    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NMT_2  -------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iyk B  60 EGPIDKLKTPEDVPNDPLPLISDFEWSTLDIDDNLQLDELYKLLYDNYVEDIDATFRFKYSHEFFQWALKPPGWRKDWHVGVRVKSTGKLVAFIAATPVTFKLNKSNKVIDSVEINFLCIHKKLRNKRLAPVLIKEITRRVNKQNIWQALYTGGSILPTPLTTCRYQHRPINWSKLHDVGFSHLPPNQTKSSMVASYTLPNNPKLKGLRPMTGKDVSTVLSLLYKYQERFDIVQLFTEEEFKHWMLGHDENSDSNVVKSYVVEDENGIITDYFSYYLLPFTVLDNAQHDELGIAYLFYYASDSFEKPNYKKRLNELITDALITSKKFGVDVFNCLTCQDNTYFLKDCKFGSGDGFLNYYLFNYRTFPMDGGIDKKTKEVVEDQTSGIGVVLL 451
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449

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

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Acyl-CoA N-acyltransferases (Nat) (250)

Superfamily: Acyl-CoA N-acyltransferases (Nat) (250)

Family: N-myristoyl transferase, NMT (7)

Protein domain: N-myristoyl transferase, NMT (7)

Yeast (Candida albicans) [TaxId: 5476] (3)

1a	d1iyka1	A:60-224
1b	d1iyka2	A:225-451
1c	d1iykb1	B:60-224
1d	d1iykb2	B:225-451

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Aminopeptidase (284)

Homologous Superfamily: [code=3.40.630.30, no name defined] (126)

Candida albicans. Organism_taxid: 5476. (2)

1a	1iykA01	A:60-206
1b	1iykB01	B:60-206
1c	1iykA02	A:207-451
1d	1iykB02	B:207-451

(no "Pfam Domain" information available for 1IYK)

Asymmetric Unit(hide GO term definitions)

Chain A,B (NMT_CANAL | P30418)

molecular function
	GO:0008144	drug binding	Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
	GO:0004379	glycylpeptide N-tetradecanoyltransferase activity	Catalysis of the reaction: tetradecanoyl-CoA + glycyl-peptide = CoA + N-tetradecanoylglycyl-peptide.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0016746	transferase activity, transferring acyl groups	Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
	GO:0018008	N-terminal peptidyl-glycine N-myristoylation	The myristoylation of the N-terminal glycine of proteins to form the derivative N-myristoyl-glycine.
	GO:0006499	N-terminal protein myristoylation	The covalent attachment of a myristoyl group to the N-terminal amino acid residue of a protein.
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	NMT_CANAL \| P30418	:	1iyl 1nmt

1iyl	1IYL CONTAINS THE SAME PROTEIN WITH NON-PEPTIDIC INHIBITOR

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