3TF6 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF NEUTROPHIL GELATINASE-ASSOCIATED LIPOCALIN (C87S MUTANT) IN COMPLEX WITH EUROPIUM AND THE SIDEROPHORE ANALOG TREN(CAM)(1,2-HOPO)2

Authors :   Seattle Structural Genomics Center For Infectious Disease (S

Date :   15 Aug 11 (Deposition) - 07 Sep 11 (Release) - 09 Oct 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

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

Keywords :   Ssgcid, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Antimicrobial Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Correnti, V. Richardson, A. K. Sia, A. D. Bandaranayake, M. Ruiz, Y. Suryo Rahmanto, Z. Kovacevic, M. C. Clifton, M. A. Holmes, B. K. Kaiser, J. Barasch, K. N. Raymond, D. R. Richardson, R. K. Strong
Siderocalin/Lcn2/Ngal/24P3 Does Not Drive Apoptosis Through Gentisic Acid Mediated Iron Withdrawal In Hematopoietic Cel Lines.
Plos One V. 7 43696 2012
PubMed-ID: 22928018 | Reference-DOI: 10.1371/JOURNAL.PONE.0043696

Molecule 1 - NEUTROPHIL GELATINASE-ASSOCIATED LIPOCALIN
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-4T3
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	LCN2, HNL, NGAL
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	NGAL, 25 KDA ALPHA-2-MICROGLOBULIN-RELATED SUBUNIT OF MMP-9, LIPOCALIN-2, ONCOGENE 24P3, P25

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 18)

No.	Name	Count	Type	Full Name
1	CL	5	Ligand/Ion	CHLORIDE ION
2	DBH	3	Ligand/Ion	2,3-DIHYDROXY-BENZOIC ACID
3	EU	3	Ligand/Ion	EUROPIUM ION
4	GOL	4	Ligand/Ion	GLYCEROL
5	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	DBH	1	Ligand/Ion	2,3-DIHYDROXY-BENZOIC ACID
3	EU	-1	Ligand/Ion	EUROPIUM ION
4	GOL	1	Ligand/Ion	GLYCEROL
5	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	DBH	1	Ligand/Ion	2,3-DIHYDROXY-BENZOIC ACID
3	EU	-1	Ligand/Ion	EUROPIUM ION
4	GOL	-1	Ligand/Ion	GLYCEROL
5	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (3, 5)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	DBH	1	Ligand/Ion	2,3-DIHYDROXY-BENZOIC ACID
3	EU	-1	Ligand/Ion	EUROPIUM ION
4	GOL	3	Ligand/Ion	GLYCEROL
5	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LEU A:42 , ASN A:164 , HIS A:165 , LYS C:75	BINDING SITE FOR RESIDUE GOL A 201
02	AC2	SOFTWARE	DBH A:216	BINDING SITE FOR RESIDUE EU A 206
03	AC3	SOFTWARE	TYR A:106 , PHE A:123 , LYS A:125 , TYR A:132 , LYS A:134 , HOH A:189 , EU A:206	BINDING SITE FOR RESIDUE DBH A 216
04	AC4	SOFTWARE	TYR A:52 , THR A:54 , SER A:68 , ARG A:81 , PHE A:123 , LYS A:134 , THR A:136 , TYR A:138	BINDING SITE FOR RESIDUE SO4 A 221
05	AC5	SOFTWARE	LYS B:125 , DBH B:216	BINDING SITE FOR RESIDUE EU B 206
06	AC6	SOFTWARE	TYR B:106 , PHE B:123 , LYS B:134 , EU B:206	BINDING SITE FOR RESIDUE DBH B 216
07	AC7	SOFTWARE	VAL B:33 , TYR B:52 , THR B:54 , ARG B:81 , PHE B:123 , LYS B:134 , THR B:136 , TYR B:138	BINDING SITE FOR RESIDUE SO4 B 221
08	AC8	SOFTWARE	LYS A:75 , LEU C:42 , ASN C:164 , HIS C:165	BINDING SITE FOR RESIDUE GOL C 201
09	AC9	SOFTWARE	DBH C:216	BINDING SITE FOR RESIDUE EU C 206
10	BC1	SOFTWARE	TYR C:106 , PHE C:123 , LYS C:125 , TYR C:132 , PHE C:133 , LYS C:134 , HOH C:197 , EU C:206	BINDING SITE FOR RESIDUE DBH C 216
11	BC2	SOFTWARE	TYR C:52 , THR C:54 , SER C:68 , ARG C:81 , PHE C:123 , LYS C:134 , TYR C:138	BINDING SITE FOR RESIDUE SO4 C 221
12	BC3	SOFTWARE	THR C:93 , LEU C:94 , ILE C:97 , SER C:105 , TYR C:106	BINDING SITE FOR RESIDUE GOL C 183
13	BC4	SOFTWARE	GLN A:117 , ASN C:114 , HIS C:118 , HOH C:232	BINDING SITE FOR RESIDUE GOL C 184
14	BC5	SOFTWARE	SER C:146	BINDING SITE FOR RESIDUE CL C 185
15	BC6	SOFTWARE	SER A:146	BINDING SITE FOR RESIDUE CL A 183
16	BC7	SOFTWARE	GLU C:163	BINDING SITE FOR RESIDUE CL C 186
17	BC8	SOFTWARE	MET C:120	BINDING SITE FOR RESIDUE CL C 187
18	BC9	SOFTWARE	LYS B:75	BINDING SITE FOR RESIDUE CL B 183

Asymmetric Unit

No.	Residues
1	A:76	-	A:175
2	B:76	-	B:175
3	C:76	-	C:175

(no "Cis Peptide Bond" information available for 3TF6)

(no "SAP(SNP)/Variant" information available for 3TF6)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIPOCALIN	PS00213	Lipocalin signature.	NGAL_HUMAN	41-54	3	A:21-34 B:21-34 C:21-34

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIPOCALIN	PS00213	Lipocalin signature.	NGAL_HUMAN	41-54	1	A:21-34 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIPOCALIN	PS00213	Lipocalin signature.	NGAL_HUMAN	41-54	1	- B:21-34 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIPOCALIN	PS00213	Lipocalin signature.	NGAL_HUMAN	41-54	1	- - C:21-34

Asymmetric Unit (6, 18)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000373017	1	ENSE00001459333	chr9:130911350-130911543	194	NGAL_HUMAN	-	0	0	-	-
1.2d	ENST00000373017	2d	ENSE00001459332	chr9:130911762-130911942	181	NGAL_HUMAN	1-46	46	3	A:3-26 B:5-26 C:5-26	24 22 22
1.3	ENST00000373017	3	ENSE00000984625	chr9:130912517-130912653	137	NGAL_HUMAN	47-92	46	3	A:27-72 B:27-72 (gaps) C:27-72	46 46 46
1.6b	ENST00000373017	6b	ENSE00000984626	chr9:130913917-130913996	80	NGAL_HUMAN	92-119	28	3	A:72-99 B:72-99 C:72-99	28 28 28
1.7	ENST00000373017	7	ENSE00000984627	chr9:130914185-130914304	120	NGAL_HUMAN	119-159	41	3	A:99-139 B:99-139 C:99-139	41 41 41
1.8	ENST00000373017	8	ENSE00001419823	chr9:130914462-130914563	102	NGAL_HUMAN	159-193	35	3	A:139-173 B:139-173 C:139-173	35 35 35
1.9b	ENST00000373017	9b	ENSE00001459311	chr9:130915379-130915412	34	NGAL_HUMAN	193-198	6	3	A:173-178 B:173-177 C:173-177	6 5 5

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:176
 aligned with NGAL_HUMAN | P80188 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:176
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192      
           NGAL_HUMAN    23 STSDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGCQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCIDG 198
               SCOP domains d3tf6a_ A: Neutrophil gelatinase-associated lipocalin (NGAL)                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh............eeeeeeeeee..............eeeeee.....eeeeeeeee..eeeeeeeeeee.....eeee.hhhhh..eeeeeeeeeee....eeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhh..hhh.ee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------LIPOCALIN     ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.2d  PDB: A:3-26  Exon 1.3  PDB: A:27-72 UniProt: 47-92         --------------------------Exon 1.7  PDB: A:99-139 UniProt: 119-159 ---------------------------------1.9b   Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------Exon 1.6b  PDB: A:72-99     ---------------------------------------Exon 1.8  PDB: A:139-173           ----- Transcript 1 (2)
                 3tf6 A   3 STSDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGSQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCIDG 178
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172

Chain B from PDB  Type:PROTEIN  Length:171
 aligned with NGAL_HUMAN | P80188 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:173
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194   
           NGAL_HUMAN    25 SDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGCQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCID 197
               SCOP domains d3tf6b_ B: Neutrophil gelatinase-associat  ed lipocalin (NGAL)                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh............eeeeeeeeee.......--.....eeeeee.....eeeeeeeee..eeeeeeeeeee.....eeee.hhhhh..eeeeeeeeeee....eeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhh..hhh.ee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------LIPOCALIN     ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2d  PDB: B:5-26Exon 1.3  PDB: B:27-72 (gaps) UniProt: 47-92  --------------------------Exon 1.7  PDB: B:99-139 UniProt: 119-159 ---------------------------------1.9b  Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------Exon 1.6b  PDB: B:72-99     ---------------------------------------Exon 1.8  PDB: B:139-173           ---- Transcript 1 (2)
                 3tf6 B   5 SDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILRED--PQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGSQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCID 177
                                    14        24        34        44|  |    54        64        74        84        94       104       114       124       134       144       154       164       174   
                                                                   45 48

Chain C from PDB  Type:PROTEIN  Length:173
 aligned with NGAL_HUMAN | P80188 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:173
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194   
           NGAL_HUMAN    25 SDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGCQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCID 197
               SCOP domains d3tf6c_ C: Neutrophil gelatinase-associated lipocalin (NGAL)                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh............eeeeeeeeee..............eeeeee.....eeeeeeeee..eeeeeeeeeee.....eeee.hhhhh..eeeeeeeeeee....eeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhh..hhh.ee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------LIPOCALIN     ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2d  PDB: C:5-26Exon 1.3  PDB: C:27-72 UniProt: 47-92         --------------------------Exon 1.7  PDB: C:99-139 UniProt: 119-159 ---------------------------------1.9b  Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------Exon 1.6b  PDB: C:72-99     ---------------------------------------Exon 1.8  PDB: C:139-173           ---- Transcript 1 (2)
                 3tf6 C   5 SDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGSQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCID 177
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174

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	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: Neutrophil gelatinase-associated lipocalin (NGAL) (28)

Human (Homo sapiens) [TaxId: 9606] (28)

1a	d3tf6a_	A:
1b	d3tf6b_	B:
1c	d3tf6c_	C:

(no "CATH Domain" information available for 3TF6)

(no "Pfam Domain" information available for 3TF6)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (NGAL_HUMAN | P80188)

molecular function
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0036094	small molecule binding	Interacting selectively and non-covalently with a small molecule, any low molecular weight, monomeric, non-encoded molecule.
	GO:0005215	transporter activity	Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0006879	cellular iron ion homeostasis	Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0055072	iron ion homeostasis	Any process involved in the maintenance of an internal steady state of iron ions within an organism or cell.
	GO:0015891	siderophore transport	The directed movement of siderophores, low molecular weight Fe(III)-chelating substances, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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:0005623	cell	The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
	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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1l6m
3hwd
3hwe
3hwg	RELATED ID: HOSA.18070.A RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 18)

Sites (18, 18)

SS Bonds (3, 3)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 3)

Exons (6, 18)

Sequences/Alignments

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SCOP Domains (1, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

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Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File