1FJ2 - JenaLib

Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE HUMAN ACYL PROTEIN THIOESTERASE 1 AT 1.5 A RESOLUTION

Authors :   Y. Devedjiev, Z. Dauter, S. Kuznetsov, T. Jones, Z. Derewenda

Date :   07 Aug 00 (Deposition) - 29 Nov 00 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Alpha/Beta Hydrolase, Serine Hydrolase, Sad, Anomalous Diffraction, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Devedjiev, Z. Dauter, S. R. Kuznetsov, T. L. Jones, Z. S. Derewenda
Crystal Structure Of The Human Acyl Protein Thioesterase I From A Single X-Ray Data Set To 1. 5 A.
Structure Fold. Des. V. 8 1137 2000
PubMed-ID: 11080636 | Reference-DOI: 10.1016/S0969-2126(00)00529-3

Molecule 1 - PROTEIN (ACYL PROTEIN THIOESTERASE 1)
	Chains	:	A, B
	EC Number	:	3.1.4.39
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		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 (1, 40)

No.	Name	Count	Type	Full Name
1	BR	40	Ligand/Ion	BROMIDE ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	BR	-1	Ligand/Ion	BROMIDE ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	BR	-1	Ligand/Ion	BROMIDE ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	BR	-1	Ligand/Ion	BROMIDE ION

Asymmetric Unit (40, 40)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LEU A:25 , SER A:114 , GLN A:115	BINDING SITE FOR RESIDUE BR A 801
02	AC2	SOFTWARE	LEU B:25 , SER B:114 , GLN B:115	BINDING SITE FOR RESIDUE BR B 802
03	AC3	SOFTWARE	ARG B:13 , THR B:16 , HIS B:43 , ILE B:224	BINDING SITE FOR RESIDUE BR B 803
04	AC4	SOFTWARE	THR A:16 , PRO A:223 , ILE A:224	BINDING SITE FOR RESIDUE BR A 804
05	AC5	SOFTWARE	ALA B:11 , HOH B:1067	BINDING SITE FOR RESIDUE BR B 805
06	AC6	SOFTWARE	ALA A:11	BINDING SITE FOR RESIDUE BR A 806
07	AC7	SOFTWARE	HOH A:905 , HOH A:974 , THR B:28	BINDING SITE FOR RESIDUE BR B 807
08	AC8	SOFTWARE	THR A:28	BINDING SITE FOR RESIDUE BR A 808
09	AC9	SOFTWARE	GLY A:200 , GLN B:207 , GLN B:208	BINDING SITE FOR RESIDUE BR B 810
10	ACA	AUTHOR	SER A:114 , ASP A:169 , HIS A:203	Active site in Chain A
11	ACB	AUTHOR	SER B:114 , ASP B:169 , HIS B:203	Active site in Chain B
12	BC1	SOFTWARE	ASN A:192	BINDING SITE FOR RESIDUE BR A 812
13	BC2	SOFTWARE	CYS A:206 , GLN A:208 , HOH A:962	BINDING SITE FOR RESIDUE BR A 813
14	BC3	SOFTWARE	PRO B:4 , LEU B:5 , THR B:197 , HOH B:1029	BINDING SITE FOR RESIDUE BR B 814
15	BC4	SOFTWARE	HOH B:847	BINDING SITE FOR RESIDUE BR B 815
16	BC5	SOFTWARE	MET A:-5 , HOH A:1030	BINDING SITE FOR RESIDUE BR A 816
17	BC6	SOFTWARE	HOH A:926	BINDING SITE FOR RESIDUE BR A 817
18	BC7	SOFTWARE	PHE A:195	BINDING SITE FOR RESIDUE BR A 818
19	BC8	SOFTWARE	HOH B:858	BINDING SITE FOR RESIDUE BR B 819
20	BC9	SOFTWARE	HOH A:977 , HOH A:990 , HOH A:1024 , CYS B:168	BINDING SITE FOR RESIDUE BR B 820
21	CC1	SOFTWARE	GLU B:199	BINDING SITE FOR RESIDUE BR B 821
22	CC2	SOFTWARE	HIS B:23 , HOH B:1036 , HOH B:1079	BINDING SITE FOR RESIDUE BR B 822
23	CC3	SOFTWARE	LEU A:5 , THR A:197	BINDING SITE FOR RESIDUE BR A 823
24	CC4	SOFTWARE	HIS A:23 , HIS A:50	BINDING SITE FOR RESIDUE BR A 824
25	CC5	SOFTWARE	ASP A:167 , GLY A:200 , ASN B:61 , GLN B:207	BINDING SITE FOR RESIDUE BR B 825
26	CC6	SOFTWARE	THR B:197	BINDING SITE FOR RESIDUE BR B 826
27	CC7	SOFTWARE	SER A:160 , HOH A:898 , HOH A:943	BINDING SITE FOR RESIDUE BR A 827
28	CC8	SOFTWARE	PRO A:75	BINDING SITE FOR RESIDUE BR A 828
29	CC9	SOFTWARE	ALA A:15 , HOH A:1011 , HOH A:1053	BINDING SITE FOR RESIDUE BR A 829
30	DC1	SOFTWARE	GLN A:86 , HOH A:963 , HOH A:1032 , HOH A:1059	BINDING SITE FOR RESIDUE BR A 830
31	DC2	SOFTWARE	CYS A:168 , MET A:202 , BR A:832 , HOH B:1048	BINDING SITE FOR RESIDUE BR A 831
32	DC3	SOFTWARE	CYS A:168 , BR A:831 , HOH B:1044 , HOH B:1048	BINDING SITE FOR RESIDUE BR A 832
33	DC4	SOFTWARE	LYS B:183 , HOH B:1020	BINDING SITE FOR RESIDUE BR B 833
34	DC5	SOFTWARE	LYS B:185 , HOH B:1009	BINDING SITE FOR RESIDUE BR B 834
35	DC6	SOFTWARE	SER B:41 , HIS B:43 , HOH B:889 , HOH B:978	BINDING SITE FOR RESIDUE BR B 835
36	DC7	SOFTWARE	ASN B:106 , HOH B:903 , HOH B:1023	BINDING SITE FOR RESIDUE BR B 836
37	DC8	SOFTWARE	GLN B:149 , HOH B:917	BINDING SITE FOR RESIDUE BR B 837
38	DC9	SOFTWARE	LYS B:92 , GLN B:128 , HOH B:1061	BINDING SITE FOR RESIDUE BR B 838
39	EC1	SOFTWARE	LYS B:100 , HOH B:851 , HOH B:1077	BINDING SITE FOR RESIDUE BR B 839
40	EC2	SOFTWARE	SER A:205	BINDING SITE FOR RESIDUE BR A 840

(no "SS Bond" information available for 1FJ2)

(no "Cis Peptide Bond" information available for 1FJ2)

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_060991	P	153	S	LYPA1_HUMAN	Polymorphism	11549448	A/B	P	148	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_060991	P	153	S	LYPA1_HUMAN	Polymorphism	11549448	A	P	148	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_060991	P	153	S	LYPA1_HUMAN	Polymorphism	11549448	B	P	148	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_060991	P	153	S	LYPA1_HUMAN	Polymorphism	11549448	A/B	P	148	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 1FJ2)

Asymmetric Unit (9, 18)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000316963	1a	ENSE00001383803	chr8:55014577-55014315	263	LYPA1_HUMAN	1-23	23	2	A:-5-18 B:-5-18	23 23
1.3a	ENST00000316963	3a	ENSE00001019707	chr8:55013499-55013468	32	LYPA1_HUMAN	24-34	11	2	A:19-29 B:19-29	11 11
1.5	ENST00000316963	5	ENSE00000980378	chr8:54978373-54978308	66	LYPA1_HUMAN	34-56	23	2	A:29-51 B:29-51	23 23
1.6	ENST00000316963	6	ENSE00001154653	chr8:54975935-54975888	48	LYPA1_HUMAN	56-72	17	2	A:51-67 B:51-67	17 17
1.7	ENST00000316963	7	ENSE00001154643	chr8:54974884-54974814	71	LYPA1_HUMAN	72-96	25	2	A:67-91 B:67-91	25 25
1.8c	ENST00000316963	8c	ENSE00001154638	chr8:54967693-54967620	74	LYPA1_HUMAN	96-120	25	2	A:91-115 B:91-115	25 25
1.10b	ENST00000316963	10b	ENSE00001154633	chr8:54965316-54965215	102	LYPA1_HUMAN	121-154	34	2	A:116-149 B:116-149	34 34
1.11c	ENST00000316963	11c	ENSE00000928383	chr8:54963748-54963572	177	LYPA1_HUMAN	155-213	59	2	A:150-208 B:150-208	59 59
1.12g	ENST00000316963	12g	ENSE00002133110	chr8:54960678-54958938	1741	LYPA1_HUMAN	214-230	17	2	A:209-224 B:209-224	16 16

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:229
 aligned with LYPA1_HUMAN | O75608 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:229
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         
          LYPA1_HUMAN     1 MCGNNMSTPLPAIVPAARKATAAVIFLHGLGDTGHGWAEAFAGIRSSHIKYICPHAPVRPVTLNMNVAMPSWFDIIGLSPDSQEDESGIKQAAENIKALIDQEVKNGIPSNRIILGGFSQGGALSLYTALTTQQKLAGVTALSCWLPLRASFPQGPIGGANRDISILQCHGDCDPLVPLMFGSLTVEKLKTLVNPANVTFKTYEGMMHSSCQQEMMDVKQFIDKLLPPI 229
               SCOP domains d1fj2a_ A: Acyl protein thioesterase 1                                                                                                                                                                                                SCOP domains
               CATH domains 1fj2A00 A:-5-224  [code=3.40.50.1820, no name defined]                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh...eee.......eeeeee.....hhhhhhhhhhh.....eeeee....eee.hhhh..eee..............hhhhhhhhhhhhhhhhhhhhhh..hhh.eeeeeehhhhhhhhhhhh.......eeeee.....hhhhh.............eeeeee......hhhhhhhhhhhhhhhhhhh.eeeeee.......hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------S---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:-5-18Exon 1.3a  ---------------------Exon 1.6         -----------------------Exon 1.8c  PDB: A:91-115 Exon 1.10b  PDB: A:116-149        Exon 1.11c  PDB: A:150-208 UniProt: 155-213                Exon 1.12g       Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.5  PDB: A:29-51 ---------------Exon 1.7  PDB: A:67-91   ------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1fj2 A  -5 MDPEFMSTPLPAIVPAARKATAAVIFLHGLGDTGHGWAEAFAGIRSSHIKYICPHAPVRPVTLNMNVAMPSWFDIIGLSPDSQEDESGIKQAAENIKALIDQEVKNGIPSNRIILGGFSQGGALSLYTALTTQQKLAGVTALSCWLPLRASFPQGPIGGANRDISILQCHGDCDPLVPLMFGSLTVEKLKTLVNPANVTFKTYEGMMHSSCQQEMMDVKQFIDKLLPPI 224
                                ||   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215         
                               -1|                                                                                                                                                                                                                               
                                 1

Chain B from PDB  Type:PROTEIN  Length:229
 aligned with LYPA1_HUMAN | O75608 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:229
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         
          LYPA1_HUMAN     1 MCGNNMSTPLPAIVPAARKATAAVIFLHGLGDTGHGWAEAFAGIRSSHIKYICPHAPVRPVTLNMNVAMPSWFDIIGLSPDSQEDESGIKQAAENIKALIDQEVKNGIPSNRIILGGFSQGGALSLYTALTTQQKLAGVTALSCWLPLRASFPQGPIGGANRDISILQCHGDCDPLVPLMFGSLTVEKLKTLVNPANVTFKTYEGMMHSSCQQEMMDVKQFIDKLLPPI 229
               SCOP domains d1fj2b_ B: Acyl protein thioesterase 1                                                                                                                                                                                                SCOP domains
               CATH domains 1fj2B00 B:-5-224  [code=3.40.50.1820, no name defined]                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh....eee.......eeeeee.....hhhhhhhhhhh.....eeeee....eee.hhhh..eee..............hhhhhhhhhhhhhhhhhhhhhh..hhh.eeeeeehhhhhhhhhhhhhh.....eeeee.....hhhhh.............eeeeee......hhhhhhhhhhhhhhhhhhh.eeeeee.......hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------S---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: B:-5-18Exon 1.3a  ---------------------Exon 1.6         -----------------------Exon 1.8c  PDB: B:91-115 Exon 1.10b  PDB: B:116-149        Exon 1.11c  PDB: B:150-208 UniProt: 155-213                Exon 1.12g       Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.5  PDB: B:29-51 ---------------Exon 1.7  PDB: B:67-91   ------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1fj2 B  -5 MDPEFMSTPLPAIVPAARKATAAVIFLHGLGDTGHGWAEAFAGIRSSHIKYICPHAPVRPVTLNMNVAMPSWFDIIGLSPDSQEDESGIKQAAENIKALIDQEVKNGIPSNRIILGGFSQGGALSLYTALTTQQKLAGVTALSCWLPLRASFPQGPIGGANRDISILQCHGDCDPLVPLMFGSLTVEKLKTLVNPANVTFKTYEGMMHSSCQQEMMDVKQFIDKLLPPI 224
                                ||   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215         
                               -1|                                                                                                                                                                                                                               
                                 1

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	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) (23833)

Fold: alpha/beta-Hydrolases (971)

Superfamily: alpha/beta-Hydrolases (971)

Family: Carboxylesterase/thioesterase 1 (8)

Protein domain: Acyl protein thioesterase 1 (1)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d1fj2a_	A:
1b	d1fj2b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1820, no name defined] (692)

Human (Homo sapiens) (118)

1a	1fj2A00	A:-5-224
1b	1fj2B00	B:-5-224

(no "Pfam Domain" information available for 1FJ2)

Asymmetric Unit(hide GO term definitions)

Chain A,B (LYPA1_HUMAN | O75608)

molecular function
	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:0016298	lipase activity	Catalysis of the hydrolysis of a lipid or phospholipid.
	GO:0004622	lysophospholipase activity	Catalysis of the reaction: 2-lysophosphatidylcholine + H2O = glycerophosphocholine + a carboxylate.
	GO:0008474	palmitoyl-(protein) hydrolase activity	Catalysis of the reaction: palmitoyl-protein + H2O = palmitate + protein.
biological process
	GO:0006631	fatty acid metabolic process	The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	GO:0042997	negative regulation of Golgi to plasma membrane protein transport	Any process that stops, prevents, or reduces the frequency, rate or extent of the transport of proteins from the Golgi to the plasma membrane.
	GO:0002084	protein depalmitoylation	The removal of palymitoyl groups from a lipoprotein.
	GO:0050999	regulation of nitric-oxide synthase activity	Any process that modulates the activity of the enzyme nitric-oxide synthase.
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.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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	1fj2
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	LYPA1_HUMAN \| O75608
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	LYPA1_HUMAN \| O75608	:	5sym

1auo	HUMAN ACYL PROTEIN THIOESTERASE 1 AND CARBOXYLESTERASE FROM PSEUDOMONAS FLUORESCENCE (1AUO) ARE 34% IDENTICAL ACCORDING TO THE SEQUENCE, HOWEVER, OVERALL FOLD OF THE BOTH ENZYMES IS CLOSE WITH R.M.S. VALUE OF 1.34 FOR 212 COMMON C-ALFA ATOMS.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 40)

Sites (40, 40)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (0, 0)

Exons (9, 18)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (13, 13)

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