1LN3 - JenaLib

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Title :   STRUCTURE OF HUMAN PHOSPHATIDYLCHOLINE TRANSFER PROTEIN IN COMPLEX WITH PALMITOYL-LINOLEOYL PHOSPHATIDYLCHOLINE (SELENO-MET PROTEIN)

Authors :   S. L. Roderick, W. W. Chan, D. S. Agate, L. R. Olsen, M. W. Vetting, K. R. Rajashankar, D. E. Cohen

Date :   02 May 02 (Deposition) - 26 Jun 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Start Domain, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. L. Roderick, W. W. Chan, D. S. Agate, L. R. Olsen, M. W. Vetting, K. R. Rajashankar, D. E. Cohen
Structure Of Human Phosphatidylcholine Transfer Protein In Complex With Its Ligand.
Nat. Struct. Biol. V. 9 507 2002
PubMed-ID: 12055623
(for further references see the PDB file header)

Molecule 1 - PHOSPHATIDYLCHOLINE TRANSFER PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PC-TP

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 14)

No.	Name	Count	Type	Full Name
1	CPL	2	Ligand/Ion	1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 7)

No.	Name	Count	Type	Full Name
1	CPL	1	Ligand/Ion	1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 7)

No.	Name	Count	Type	Full Name
1	CPL	1	Ligand/Ion	1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:33 , VAL A:34 , TYR A:54 , LEU A:68 , TYR A:72 , ARG A:78 , TRP A:101 , VAL A:103 , TYR A:114 , TYR A:116 , GLN A:157 , LEU A:159 , MSE A:173 , TYR A:175 , TRP A:190 , ALA A:191 , VAL A:196 , PHE A:199 , LEU A:200 , HOH A:2013	BINDING SITE FOR RESIDUE CPL A 300
2	AC2	SOFTWARE	LEU B:33 , ILE B:41 , TYR B:54 , VAL B:56 , TYR B:72 , ARG B:78 , TYR B:84 , TRP B:101 , VAL B:103 , TYR B:105 , TYR B:114 , TYR B:116 , TYR B:155 , GLN B:157 , LEU B:159 , MSE B:173 , TYR B:175 , VAL B:196 , PHE B:199	BINDING SITE FOR RESIDUE CPL B 301

Asymmetric Unit

No.	Residues
1	A:63	-	A:207

Asymmetric Unit

No.	Residues
1	Phe A:107	-	Pro A:108
2	Phe B:107	-	Pro B:108

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_052070	E	10	A	PPCT_HUMAN	Polymorphism	12941739	A/B	E	10	A

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_052070	E	10	A	PPCT_HUMAN	Polymorphism	12941739	A	E	10	A

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_052070	E	10	A	PPCT_HUMAN	Polymorphism	12941739	B	E	10	A

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

(no "PROSITE Motif" information available for 1LN3)

Asymmetric Unit (6, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000268896	1a	ENSE00001302376	chr17:53828356-53828605	250	PPCT_HUMAN	1-47	47	2	A:8-47 B:8-47	40 40
1.2	ENST00000268896	2	ENSE00001731482	chr17:53844696-53844813	118	PPCT_HUMAN	48-87	40	2	A:48-87 B:48-87	40 40
1.3	ENST00000268896	3	ENSE00001247504	chr17:53848467-53848546	80	PPCT_HUMAN	87-113	27	2	A:87-113 B:87-113	27 27
1.4	ENST00000268896	4	ENSE00001316597	chr17:53851085-53851256	172	PPCT_HUMAN	114-171	58	2	A:114-171 B:114-171	58 58
1.5	ENST00000268896	5	ENSE00000946954	chr17:53852153-53852220	68	PPCT_HUMAN	171-193	23	2	A:171-193 B:171-193	23 23
1.6b	ENST00000268896	6b	ENSE00001376208	chr17:53853396-53854748	1353	PPCT_HUMAN	194-214	21	2	A:194-210 B:194-210	17 17

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
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Chain A from PDB  Type:PROTEIN  Length:203
 aligned with PPCT_HUMAN | Q9UKL6 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:203
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207   
           PPCT_HUMAN     8 FSEEQFWEACAELQQPALAGADWQLLVETSGISIYRLLDKKTGLYEYKVFGVLEDCSPTLLADIYMDSDYRKQWDQYVKELYEQECNGETVVYWEVKYPFPMSNRDYVYLRQRRDLDMEGRKIHVILARSTSMPQLGERSGVIRVKQYKQSLAIESDGKKGSKVFMYYFDNPGGQIPSWLINWAAKNGVPNFLKDMARACQNY 210
               SCOP domains d1ln3a_ A: Phosphatidylcholine transfer protein                                                                                                                                                             SCOP domains
               CATH domains 1ln3A00 A:8-210  [code=3.30.530.20, no name defined]                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh............ee..eeeeeeee....eeeeeeeeee...hhhhhhhhhhhhhhhhhhh..eeeeeeeee..eeeeeeee........eeeeeeeeeeeehhhhh.eeeeeeee............eee..eeeeeeeee.....eeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:8-47 UniProt: 1-47    Exon 1.2  PDB: A:48-87 UniProt: 48-87   --------------------------Exon 1.4  PDB: A:114-171 UniProt: 114-171                 ----------------------Exon 1.6b         Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------Exon 1.3  PDB: A:87-113    ---------------------------------------------------------Exon 1.5  PDB: A:171-19----------------- Transcript 1 (2)
                 1ln3 A   8 FSEEQFWEACAELQQPALAGADWQLLVETSGISIYRLLDKKTGLYEYKVFGVLEDCSPTLLADIYmDSDYRKQWDQYVKELYEQECNGETVVYWEVKYPFPmSNRDYVYLRQRRDLDmEGRKIHVILARSTSmPQLGERSGVIRVKQYKQSLAIESDGKKGSKVFmYYFDNPGGQIPSWLINWAAKNGVPNFLKDmARACQNY 210
                                    17        27        37        47        57        67     |  77        87        97       107 |     117       127       137  |    147       157       167     | 177       187       197     | 207   
                                                                                            73-MSE                             109-MSE         125-MSE        140-MSE                          173-MSE                       203-MSE

Chain B from PDB  Type:PROTEIN  Length:203
 aligned with PPCT_HUMAN | Q9UKL6 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:203
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207   
           PPCT_HUMAN     8 FSEEQFWEACAELQQPALAGADWQLLVETSGISIYRLLDKKTGLYEYKVFGVLEDCSPTLLADIYMDSDYRKQWDQYVKELYEQECNGETVVYWEVKYPFPMSNRDYVYLRQRRDLDMEGRKIHVILARSTSMPQLGERSGVIRVKQYKQSLAIESDGKKGSKVFMYYFDNPGGQIPSWLINWAAKNGVPNFLKDMARACQNY 210
               SCOP domains d1ln3b_ B: Phosphatidylcholine transfer protein                                                                                                                                                             SCOP domains
               CATH domains 1ln3B00 B:8-210  [code=3.30.530.20, no name defined]                                                                                                                                                        CATH domains
           Pfam domains (1) --START-1ln3B01 B:10-210                                                                                                                                                                                    Pfam domains (1)
           Pfam domains (2) --START-1ln3B02 B:10-210                                                                                                                                                                                    Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhh........eeeee...eeeeeee......eeeeeeeee...hhhhhhhhhhhhhhhhhhh..eeeeeeeee..eeeeeeee........eeeeeeeeeeeehhhhh.eeeeeeee............eee..eeeeeeeee.....eeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: B:8-47 UniProt: 1-47    Exon 1.2  PDB: B:48-87 UniProt: 48-87   --------------------------Exon 1.4  PDB: B:114-171 UniProt: 114-171                 ----------------------Exon 1.6b         Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------Exon 1.3  PDB: B:87-113    ---------------------------------------------------------Exon 1.5  PDB: B:171-19----------------- Transcript 1 (2)
                 1ln3 B   8 FSEEQFWEACAELQQPALAGADWQLLVETSGISIYRLLDKKTGLYEYKVFGVLEDCSPTLLADIYmDSDYRKQWDQYVKELYEQECNGETVVYWEVKYPFPmSNRDYVYLRQRRDLDmEGRKIHVILARSTSmPQLGERSGVIRVKQYKQSLAIESDGKKGSKVFmYYFDNPGGQIPSWLINWAAKNGVPNFLKDmARACQNY 210
                                    17        27        37        47        57        67     |  77        87        97       107 |     117       127       137  |    147       157       167     | 177       187       197     | 207   
                                                                                            73-MSE                             109-MSE         125-MSE        140-MSE                          173-MSE                       203-MSE

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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

Fold: TBP-like (289)

Superfamily: Bet v1-like (158)

Family: STAR domain (6)

Protein domain: Phosphatidylcholine transfer protein (3)

Human (Homo sapiens) [TaxId: 9606] (3)

1a	d1ln3a_	A:
1b	d1ln3b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

)

Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 (47)

Homologous Superfamily: [code=3.30.530.20, no name defined] (47)

Human (Homo sapiens) (6)

1a	1ln3A00	A:8-210
1b	1ln3B00	B:8-210

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Bet_V_1_like (93)

Family: START (8)

Homo sapiens (Human) (6)

1a	START-1ln3B01	B:10-210
1b	START-1ln3B02	B:10-210

Asymmetric Unit(hide GO term definitions)

Chain A,B (PPCT_HUMAN | Q9UKL6)

molecular function
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	GO:0031210	phosphatidylcholine binding	Interacting selectively and non-covalently with phosphatidylcholine, a class of glycophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of choline.
	GO:0008525	phosphatidylcholine transporter activity	Enables the directed movement of phosphatidylcholine into, out of or within a cell, or between cells. Phosphatidylcholine refers to a class of glycerophospholipids in which the phosphatidyl group is esterified to the hydroxyl group of choline.
	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:0006869	lipid transport	The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
	GO:0015914	phospholipid transport	The directed movement of phospholipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Phospholipids are any lipids containing phosphoric acid as a mono- or diester.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
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
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	PPCT_HUMAN \| Q9UKL6	:	1ln1 1ln2

1ln1	CRYSTAL STRUCTURE OF HUMAN PHOSPHATIDYLCHOLINE TRANSFER PROTEIN IN COMPLEX WITH DILINOLEOYLPHOSPHATIDYLCHOLINE
1ln2	CRYSTAL STRUCTURE OF HUMAN PHOSPHATIDYLCHOLINE TRANSFER PROTEIN IN COMPLEX WITH DILINOLEOYLPHOSPHATIDYLCHOLINE (SELENO-MET PROTEIN)

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