3EYC - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   NEW CRYSTAL STRUCTURE OF HUMAN TEAR LIPOCALIN IN COMPLEX WITH 1,4-BUTANEDIOL IN SPACE GROUP P21

Authors :   D. A. Breustedt, L. Keil, A. Skerra

Date :   20 Oct 08 (Deposition) - 06 Oct 09 (Release) - 06 Oct 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Transport Protein, Ligand-Binding Protein, Beta-Barrel, Secreted, Sensory Transduction, Taste, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. A. Breustedt, L. Chatwell, A. Skerra
A New Crystal Form Of Human Tear Lipocalin Reveals High Flexibility In The Loop Region And Induced Fit In The Ligand Cavity
Acta Crystallogr. , Sect. D V. 65 1118 2009
PubMed-ID: 19770509 | Reference-DOI: 10.1107/S0907444909031011
(for further references see the PDB file header)

Molecule 1 - LIPOCALIN-1
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTLC3
	Expression System Strain	:	JM83
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 5-166
	Gene	:	LCN1
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	VON EBNER GLAND PROTEIN, VEG PROTEIN, TEAR PREALBUMIN, TP, TEAR LIPOCALIN, TLC

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	BU1	4	Ligand/Ion	1,4-BUTANEDIOL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	BU1	1	Ligand/Ion	1,4-BUTANEDIOL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	BU1	1	Ligand/Ion	1,4-BUTANEDIOL

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	BU1	1	Ligand/Ion	1,4-BUTANEDIOL

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	BU1	1	Ligand/Ion	1,4-BUTANEDIOL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET A:39 , PHE A:99 , HOH A:169	BINDING SITE FOR RESIDUE BU1 A 1
2	AC2	SOFTWARE	MET B:39 , LEU B:41 , PHE B:99 , HOH B:167	BINDING SITE FOR RESIDUE BU1 B 1
3	AC3	SOFTWARE	VAL C:13 , MET C:39 , LEU C:41 , PHE C:99	BINDING SITE FOR RESIDUE BU1 C 1
4	AC4	SOFTWARE	MET D:39 , LEU D:41 , PHE D:99 , HOH D:191	BINDING SITE FOR RESIDUE BU1 D 1

Asymmetric Unit

No.	Residues
1	A:61	-	A:153
2	B:61	-	B:153
3	C:61	-	C:153
4	D:61	-	D:153

(no "Cis Peptide Bond" information available for 3EYC)

(no "SAP(SNP)/Variant" information available for 3EYC)

(no "PROSITE Motif" information available for 3EYC)

Asymmetric Unit (6, 22)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000371781	1b	ENSE00001456083	chr9:138413301-138413433	133	LCN1_HUMAN	1-30	30	2	- B:12-12 C:12-12 -	- 1 1 -
1.2	ENST00000371781	2	ENSE00001791131	chr9:138413893-138414023	131	LCN1_HUMAN	31-74	44	4	A:13-56 B:13-56 (gaps) C:13-56 (gaps) D:13-56 (gaps)	44 44 44 44
1.3	ENST00000371781	3	ENSE00000828356	chr9:138415078-138415148	71	LCN1_HUMAN	74-98	25	4	A:56-80 B:56-80 C:56-80 D:56-80	25 25 25 25
1.4	ENST00000371781	4	ENSE00000828355	chr9:138415726-138415836	111	LCN1_HUMAN	98-135	38	4	A:80-117 B:80-117 C:80-117 (gaps) D:80-117 (gaps)	38 38 38 38
1.5	ENST00000371781	5	ENSE00001708103	chr9:138416676-138416777	102	LCN1_HUMAN	135-169	35	4	A:117-151 B:117-151 C:117-151 D:117-151	35 35 35 35
1.6	ENST00000371781	6	ENSE00000828353	chr9:138416978-138417004	27	LCN1_HUMAN	169-176	8	4	A:151-155 B:151-154 C:151-154 D:151-154	5 4 4 4
1.7a	ENST00000371781	7a	ENSE00001347956	chr9:138418190-138418378	189	LCN1_HUMAN	-	0	0	-	-

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:143
 aligned with LCN1_HUMAN | P31025 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:143
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170   
           LCN1_HUMAN    31 VSGTWYLKAMTVDREFPEMNLESVTPMTLTTLEGGNLEAKVTMLISGRCQEVKAVLEKTDEPGKYTADGGKHVAYIIRSHVKDHYIFYCEGELHGKPVRGVKLVGRDPKNNLEALEDFEKAAGARGLSTESILIPRQSETCSP 173
               SCOP domains d3eyca_ A: Von Ebner's gland protein (VEGP, tear lipocalin)                                                                                     SCOP domains
               CATH domains 3eycA00 A:13-155  [code=2.40.128.20, no name defined]                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee........eeee..eeeee.....eeeeeeeee..eeeeeeeeeee.....eeee....eeeeeee.eeeeeeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhh.....eee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:13-56 UniProt: 31-74       -----------------------Exon 1.4  PDB: A:80-117               ---------------------------------1.6   Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.3  PDB: A:56-80   ------------------------------------Exon 1.5  PDB: A:117-151           ---- Transcript 1 (2)
                 3eyc A  13 VSGTWYLKAMTVDREFPEMNLESVTPMTLTTLEGGNLEAKVTMLISGRCQEVKAVLEKTDEPGKYTADGGKHVAYIIRSHVKDHYIFYSEGELHGKPVRGVKLVGRDPKNNLEALEDFEKAAGARGLSTESILIPRQSETCSP 155
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152

Chain B from PDB  Type:PROTEIN  Length:140
 aligned with LCN1_HUMAN | P31025 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:143
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169   
           LCN1_HUMAN    30 DVSGTWYLKAMTVDREFPEMNLESVTPMTLTTLEGGNLEAKVTMLISGRCQEVKAVLEKTDEPGKYTADGGKHVAYIIRSHVKDHYIFYCEGELHGKPVRGVKLVGRDPKNNLEALEDFEKAAGARGLSTESILIPRQSETCS 172
               SCOP domains d3eycb_ B: Von Ebner's gland prot   ein (VEGP, tear lipocalin)                                                                                  SCOP domains
               CATH domains 3eycB00 B:12-154  [code=2.40.128.   20, no name defined]                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee........eeee..eeee..---.eeeeeeeee..eeeeeeeeeee.....eeee....eeeeeee.eeeeeeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhh.....eee..ee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1Exon 1.2  PDB: B:13-56 (gaps) UniProt: 31-74-----------------------Exon 1.4  PDB: B:80-117               ---------------------------------1.6  Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.3  PDB: B:56-80   ------------------------------------Exon 1.5  PDB: B:117-151           --- Transcript 1 (2)
                 3eyc B  12 DVSGTWYLKAMTVDREFPEMNLESVTPMTLTTL---NLEAKVTMLISGRCQEVKAVLEKTDEPGKYTADGGKHVAYIIRSHVKDHYIFYSEGELHGKPVRGVKLVGRDPKNNLEALEDFEKAAGARGLSTESILIPRQSETCS 154
                                    21        31        41  |   | 51        61        71        81        91       101       111       121       131       141       151   
                                                           44  48

Chain C from PDB  Type:PROTEIN  Length:137
 aligned with LCN1_HUMAN | P31025 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:143
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169   
           LCN1_HUMAN    30 DVSGTWYLKAMTVDREFPEMNLESVTPMTLTTLEGGNLEAKVTMLISGRCQEVKAVLEKTDEPGKYTADGGKHVAYIIRSHVKDHYIFYCEGELHGKPVRGVKLVGRDPKNNLEALEDFEKAAGARGLSTESILIPRQSETCS 172
               SCOP domains d3eycc_ C: Von E   bner's gland protein (VEGP, tear lipocalin)                                                                                  SCOP domains
               CATH domains 3eycC00 C:12-154     [code=2.40.128.20, no name defined]                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee....---..eeee..eeeee.....eeeeeeeee..eeeeeeeeeee.....eeee....eeeeeee.eeeeeeeeeeee.---..eeeeeeee.....hhhhhhhhhhhhhhh......ee..ee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1Exon 1.2  PDB: C:13-56 (gaps) UniProt: 31-74-----------------------Exon 1.4  PDB: C:80-117 (gaps)        ---------------------------------1.6  Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.3  PDB: C:56-80   ------------------------------------Exon 1.5  PDB: C:117-151           --- Transcript 1 (2)
                 3eyc C  12 DVSGTWYLKAMTVDRE---MNLESVTPMTLTTLEGGNLEAKVTMLISGRCQEVKAVLEKTDEPGKYTADGGKHVAYIIRSHVKDHYIFYSEGE---KPVRGVKLVGRDPKNNLEALEDFEKAAGARGLSTESILIPRQSETCS 154
                                    21     |  31        41        51        61        71        81        91       101  |   |111       121       131       141       151   
                                          27  31                                                                      104 108

Chain D from PDB  Type:PROTEIN  Length:137
 aligned with LCN1_HUMAN | P31025 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:142
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170  
           LCN1_HUMAN    31 VSGTWYLKAMTVDREFPEMNLESVTPMTLTTLEGGNLEAKVTMLISGRCQEVKAVLEKTDEPGKYTADGGKHVAYIIRSHVKDHYIFYCEGELHGKPVRGVKLVGRDPKNNLEALEDFEKAAGARGLSTESILIPRQSETCS 172
               SCOP domains d3eycd_ D: Von E   bner's gland protein (VEGP, tear lipocalin)                                                                                 SCOP domains
               CATH domains 3eycD00 D:13-154     [code=2.40.128.20, no name defined]                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee....---.eeee..eeeee.....eeeeeeeee..eeeeeeeee.......eeee....eeeeeee.eeeeeeeeeeee..--..eeeeeeee.....hhhhhhhhhhhhhhh.....eee..ee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: D:13-56 (gaps) UniProt: 31-74-----------------------Exon 1.4  PDB: D:80-117 (gaps)        ---------------------------------1.6  Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.3  PDB: D:56-80   ------------------------------------Exon 1.5  PDB: D:117-151           --- Transcript 1 (2)
                 3eyc D  13 VSGTWYLKAMTVDREF---NLESVTPMTLTTLEGGNLEAKVTMLISGRCQEVKAVLEKTDEPGKYTADGGKHVAYIIRSHVKDHYIFYSEGEL--KPVRGVKLVGRDPKNNLEALEDFEKAAGARGLSTESILIPRQSETCS 154
                                    22     |  32        42        52        62        72        82        92       102  |  | 112       122       132       142       152  
                                          28  32                                                                      105  |                                              
                                                                                                                         108

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: All beta proteins (24004)

Fold: Lipocalins (514)

Superfamily: Lipocalins (514)

Family: Retinol binding protein-like (261)

Protein domain: Von Ebner's gland protein (VEGP, tear lipocalin) (2)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d3eyca_	A:
1b	d3eycb_	B:
1c	d3eycc_	C:
1d	d3eycd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Lipocalin (526)

Homologous Superfamily: [code=2.40.128.20, no name defined] (352)

Human (Homo sapiens) (91)

1a	3eycA00	A:13-155
1b	3eycB00	B:12-154
1c	3eycC00	C:12-154
1d	3eycD00	D:13-154

(no "Pfam Domain" information available for 3EYC)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (LCN1_HUMAN | P31025)

molecular function
	GO:0004869	cysteine-type endopeptidase inhibitor activity	Stops, prevents or reduces the activity of a cysteine-type endopeptidase, any enzyme that hydrolyzes peptide bonds in polypeptides by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
biological process
	GO:0015909	long-chain fatty acid transport	The directed movement of long-chain fatty acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A long-chain fatty acid is a fatty acid with a chain length between C13 and C22.
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0050896	response to stimulus	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
	GO:0001895	retina homeostasis	A tissue homeostatic process involved in the maintenance of an internal equilibrium within the retina of the eye, including control of cellular proliferation and death and control of metabolic function.
	GO:0050909	sensory perception of taste	The series of events required for an organism to receive a gustatory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Gustation involves the direct detection of chemical composition, usually through contact with chemoreceptor cells. This is a neurological process.
	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: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:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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	LCN1_HUMAN \| P31025	:	1xki 4qaf

1xki	THE SAME PROTEIN CRYSTALLIZED IN SPACE GROUP C2

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (4, 4)

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