3PED - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   SIDEROCALIN RECOGNITIN OF CARBOXYMYCOBACTINS: INTERFERENCE BY THE IMMUNE SYSTEM IN INTRACELLULAR IRON ACQUISITION BY MYCOBACTERIA TUBERCULOSIS

Authors :   M. C. Clifton

Date :   25 Oct 10 (Deposition) - 05 Oct 11 (Release) - 05 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   8-Stranded Anti-Parallel Beta Barrel, Siderocalin, Siderophore Binding, Antimicrobial Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. M. Hoette, M. C. Clifton, A. M. Zawadzka, M. A. Holmes, R. K. Strong, K. R. Raymond
Siderocalin Recognitin Of Carboxymycobactins: Interference By The Immune System In Intracellular Iron Acquisition By Mycobacteria Tuberculosis
To Be Published
PubMed: search

Molecule 1 - NEUTROPHIL GELATINASE-ASSOCIATED LIPOCALIN
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 21 TO 198
	Gene	:	LCN2, HNL, NGAL
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SIDEROCALIN, 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 (3, 7)

No.	Name	Count	Type	Full Name
1	FE	3	Ligand/Ion	FE (III) ION
2	SO4	1	Ligand/Ion	SULFATE ION
3	ZYF	3	Ligand/Ion	(9Z)-11-{HYDROXY[(5S)-6-{[(1S)-3-{[(3S)-1-HYDROXY-2-OXOAZEPAN-3-YL]AMINO}-1-METHYL-3-OXOPROPYL]OXY}-5-({[(4S)-2-(2-HYDROXYPHENYL)-4,5-DIHYDRO-1,3-OXAZOL-4-YL]CARBONYL}AMINO)-6-OXOHEXYL]AMINO}-11-OXOUNDEC-9-ENOIC ACID

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	FE	-1	Ligand/Ion	FE (III) ION
2	SO4	-1	Ligand/Ion	SULFATE ION
3	ZYF	1	Ligand/Ion	(9Z)-11-{HYDROXY[(5S)-6-{[(1S)-3-{[(3S)-1-HYDROXY-2-OXOAZEPAN-3-YL]AMINO}-1-METHYL-3-OXOPROPYL]OXY}-5-({[(4S)-2-(2-HYDROXYPHENYL)-4,5-DIHYDRO-1,3-OXAZOL-4-YL]CARBONYL}AMINO)-6-OXOHEXYL]AMINO}-11-OXOUNDEC-9-ENOIC ACID

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	FE	-1	Ligand/Ion	FE (III) ION
2	SO4	-1	Ligand/Ion	SULFATE ION
3	ZYF	1	Ligand/Ion	(9Z)-11-{HYDROXY[(5S)-6-{[(1S)-3-{[(3S)-1-HYDROXY-2-OXOAZEPAN-3-YL]AMINO}-1-METHYL-3-OXOPROPYL]OXY}-5-({[(4S)-2-(2-HYDROXYPHENYL)-4,5-DIHYDRO-1,3-OXAZOL-4-YL]CARBONYL}AMINO)-6-OXOHEXYL]AMINO}-11-OXOUNDEC-9-ENOIC ACID

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	FE	-1	Ligand/Ion	FE (III) ION
2	SO4	1	Ligand/Ion	SULFATE ION
3	ZYF	1	Ligand/Ion	(9Z)-11-{HYDROXY[(5S)-6-{[(1S)-3-{[(3S)-1-HYDROXY-2-OXOAZEPAN-3-YL]AMINO}-1-METHYL-3-OXOPROPYL]OXY}-5-({[(4S)-2-(2-HYDROXYPHENYL)-4,5-DIHYDRO-1,3-OXAZOL-4-YL]CARBONYL}AMINO)-6-OXOHEXYL]AMINO}-11-OXOUNDEC-9-ENOIC ACID

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ZYF A:200	BINDING SITE FOR RESIDUE FE A 179
2	AC2	SOFTWARE	TYR A:52 , THR A:54 , VAL A:66 , SER A:68 , LEU A:70 , TRP A:79 , ARG A:81 , PHE A:123 , LYS A:125 , LYS A:134 , TYR A:138 , FE A:179 , HOH A:182 , HOH A:223	BINDING SITE FOR RESIDUE ZYF A 200
3	AC3	SOFTWARE	ZYF B:200	BINDING SITE FOR RESIDUE FE B 179
4	AC4	SOFTWARE	TYR B:52 , THR B:54 , SER B:68 , TRP B:79 , ARG B:81 , PHE B:83 , LYS B:125 , PHE B:133 , LYS B:134 , TYR B:138 , FE B:179 , HOH B:184 , HOH B:196 , HOH B:197	BINDING SITE FOR RESIDUE ZYF B 200
5	AC5	SOFTWARE	ZYF C:200	BINDING SITE FOR RESIDUE FE C 179
6	AC6	SOFTWARE	TYR C:52 , THR C:54 , SER C:68 , LEU C:70 , TRP C:79 , PHE C:123 , LYS C:125 , PHE C:133 , LYS C:134 , TYR C:138 , FE C:179	BINDING SITE FOR RESIDUE ZYF C 200
7	AC7	SOFTWARE	GLN A:117 , ASN C:114 , HOH C:246 , HOH C:252	BINDING SITE FOR RESIDUE SO4 C 180

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 3PED)

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

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:2-26 B:5-26 C:6-26	25 22 21
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:177
 aligned with NGAL_HUMAN | P80188 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:177
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       
           NGAL_HUMAN    22 DSTSDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGCQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCIDG 198
               SCOP domains d3peda_ A: Neutrophil gelatinase-associated lipocalin (NGAL)                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh......hhhhhheeeeeeeeee..............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:2-26   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)
                 3ped A   2 DSTSDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGSQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCIDG 178
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171

Chain B from PDB  Type:PROTEIN  Length:172
 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 d3pedb_ B: Neutrophil gelatinase-associa ted lipocalin (NGAL)                                                                                                                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh......hhhhhheeeeeeeeee......-.......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)
                 3ped B   5 SDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILRE-KDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGSQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCID 177
                                    14        24        34        44 |      54        64        74        84        94       104       114       124       134       144       154       164       174   
                                                                  44 |                                                                                                                                   
                                                                    46

Chain C from PDB  Type:PROTEIN  Length:172
 aligned with NGAL_HUMAN | P80188 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:172
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195  
           NGAL_HUMAN    26 DLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGCQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCID 197
               SCOP domains d3pedc_ C: Neutrophil gelatinase-associated lipocalin (NGAL)                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh......hhhhhheeeeeeeeee..............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:6-2Exon 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)
                 3ped C   6 DLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGSQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCID 177
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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	d3peda_	A:
1b	d3pedb_	B:
1c	d3pedc_	C:

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

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

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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	Cis Peptide Bonds
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	3ped
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

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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Gene Ontology (15, 15)

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Related Entries Specified in the PDB File