3CMP - 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 :   CRYSTAL STRUCTURE OF SIDEROCALIN (NGAL, LIPOCALIN 2) K125A MUTANT COMPLEXED WITH FERRIC ENTEROBACTIN

Authors :   M. C. Clifton, R. K. Strong

Date :   24 Mar 08 (Deposition) - 12 May 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Lipocalin, Siderocalin, Enterobactin, Siderophore, Iron, Glycoprotein, Pyrrolidone Carboxylic Acid, Secreted, Antimicrobial Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. C. Clifton, J. C. Pizzaro, R. Abergel, T. Hoette, V. Vigdorovich, K. Raymond, R. K. Strong
Structural Studies Of Human Siderocalin
To Be Published
PubMed: search

Molecule 1 - NEUTROPHIL GELATINASE-ASSOCIATED LIPOCALIN
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-4T3
	Expression System Strain	:	BL21DE3+RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	LCN2, HNL, NGAL
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	NGAL, P25, 25 KDA ALPHA-2-MICROGLOBULIN-RELATED SUBUNIT OF MMP-9, LIPOCALIN-2, ONCOGENE 24P3

		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 (6, 20)

No.	Name	Count	Type	Full Name
1	DBH	2	Ligand/Ion	2,3-DIHYDROXY-BENZOIC ACID
2	EB4	2	Ligand/Ion	N,N',N''-[(3S,7S,11S)-2,6,10-TRIOXO-1,5,9-TRIOXACYCLODODECANE-3,7,11-TRIYL]TRIS(2,3-DIHYDROXYBENZAMIDE)
3	FE	3	Ligand/Ion	FE (III) ION
4	GOL	3	Ligand/Ion	GLYCEROL
5	NA	7	Ligand/Ion	SODIUM ION
6	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	DBH	-1	Ligand/Ion	2,3-DIHYDROXY-BENZOIC ACID
2	EB4	1	Ligand/Ion	N,N',N''-[(3S,7S,11S)-2,6,10-TRIOXO-1,5,9-TRIOXACYCLODODECANE-3,7,11-TRIYL]TRIS(2,3-DIHYDROXYBENZAMIDE)
3	FE	-1	Ligand/Ion	FE (III) ION
4	GOL	1	Ligand/Ion	GLYCEROL
5	NA	-1	Ligand/Ion	SODIUM ION
6	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	DBH	2	Ligand/Ion	2,3-DIHYDROXY-BENZOIC ACID
2	EB4	-1	Ligand/Ion	N,N',N''-[(3S,7S,11S)-2,6,10-TRIOXO-1,5,9-TRIOXACYCLODODECANE-3,7,11-TRIYL]TRIS(2,3-DIHYDROXYBENZAMIDE)
3	FE	-1	Ligand/Ion	FE (III) ION
4	GOL	-1	Ligand/Ion	GLYCEROL
5	NA	-1	Ligand/Ion	SODIUM ION
6	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 3 (3, 4)

No.	Name	Count	Type	Full Name
1	DBH	-1	Ligand/Ion	2,3-DIHYDROXY-BENZOIC ACID
2	EB4	1	Ligand/Ion	N,N',N''-[(3S,7S,11S)-2,6,10-TRIOXO-1,5,9-TRIOXACYCLODODECANE-3,7,11-TRIYL]TRIS(2,3-DIHYDROXYBENZAMIDE)
3	FE	-1	Ligand/Ion	FE (III) ION
4	GOL	2	Ligand/Ion	GLYCEROL
5	NA	-1	Ligand/Ion	SODIUM ION
6	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	EB4 A:183	BINDING SITE FOR RESIDUE FE A 179
02	AC2	SOFTWARE	TYR A:52 , LYS A:134 , EB4 A:183	BINDING SITE FOR RESIDUE NA A 180
03	AC3	SOFTWARE	VAL A:33 , TYR A:52 , THR A:54 , SER A:68 , ARG A:81 , PHE A:123 , LYS A:134 , THR A:136 , TYR A:138 , EB4 A:183	BINDING SITE FOR RESIDUE SO4 A 181
04	AC4	SOFTWARE	ASN A:164 , HIS A:165 , HOH A:189 , HOH A:201 , LYS C:75	BINDING SITE FOR RESIDUE SO4 A 182
05	AC5	SOFTWARE	LYS B:134 , DBH B:303 , DBH B:304	BINDING SITE FOR RESIDUE FE B 179
06	AC6	SOFTWARE	THR B:54	BINDING SITE FOR RESIDUE NA B 180
07	AC7	SOFTWARE	EB4 C:186	BINDING SITE FOR RESIDUE FE C 179
08	AC8	SOFTWARE	THR C:54 , TYR C:138	BINDING SITE FOR RESIDUE NA C 180
09	AC9	SOFTWARE	TYR C:52 , LYS C:134	BINDING SITE FOR RESIDUE NA C 181
10	AD1	SOFTWARE	ALA A:40 , TRP A:79 , LEU A:103 , TYR A:106 , PHE A:123 , SER A:127 , TYR A:132 , LYS A:134 , FE A:179 , NA A:180 , SO4 A:181 , HOH A:185 , HOH A:193	BINDING SITE FOR RESIDUE EB4 A 183
11	AD2	SOFTWARE	ALA C:40 , ARG C:72 , TRP C:79 , LEU C:103 , TYR C:106 , PHE C:123 , SER C:127 , TYR C:132 , LYS C:134 , FE C:179 , GOL C:188 , HOH C:189	BINDING SITE FOR RESIDUE EB4 C 186
12	BC1	SOFTWARE	LYS A:75 , ASN C:164 , HIS C:165	BINDING SITE FOR RESIDUE SO4 C 185
13	BC3	SOFTWARE	ALA B:40 , TYR B:106 , PHE B:123 , LYS B:134 , FE B:179 , DBH B:304	BINDING SITE FOR RESIDUE DBH B 303
14	BC4	SOFTWARE	FE B:179 , DBH B:303	BINDING SITE FOR RESIDUE DBH B 304
15	BC6	SOFTWARE	ASN A:114 , HIS A:118 , ASN B:116 , ASN C:116	BINDING SITE FOR RESIDUE GOL A 184
16	BC7	SOFTWARE	GLY C:86 , SER C:87 , ILE C:97 , SER C:105 , TYR C:106	BINDING SITE FOR RESIDUE GOL C 187
17	BC8	SOFTWARE	EB4 C:186 , HOH C:231	BINDING SITE FOR RESIDUE GOL C 188

Asymmetric Unit

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

Asymmetric Unit

No.	Residues
1	Ser B:5	-	Asp B:6
2	Lys B:73	-	Lys B:74

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

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:5-26 B:5-26 C:4-26	22 22 23
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 (gaps) 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:173-178 C:173-177	6 6 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:174
 aligned with NGAL_HUMAN | P80188 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:174
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194    
           NGAL_HUMAN    25 SDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGCQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCIDG 198
               SCOP domains d3cmpa_ A: Neutrophil gelatinase-associated lipocalin (NGAL)                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhh............eeeeeeeeee..............eeee.......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:5-26Exon 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)
                 3cmp A   5 SDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGSQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKAVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCIDG 178
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174

Chain B from PDB  Type:PROTEIN  Length:168
 aligned with NGAL_HUMAN | P80188 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:174
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194    
           NGAL_HUMAN    25 SDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGCQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCIDG 198
               SCOP domains d3cmpb_ B: Neutrophil gelatinase-associa   ted lipocalin (NGAL)                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhh......hhhhhheeeee..eee......---.....eeeeee.....eeeeeeeee..eeeeee..eee.....eeee.hhhhh..eeeeeeeeeee....eeeeeeeeee..eeeeeeeeee........---.hhhhhhh...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 (gaps)    ----- Transcript 1 (2)
                 3cmp B   5 SDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILRE---PQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGSQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKAVSQNREYFKITLYGRTKELTSE---NFIRFSKSLGLPENHIVFPVPIDQCIDG 178
                                    14        24        34        44   |    54        64        74        84        94       104       114       124       134       144  |   |154       164       174    
                                                                  44  48                                                                                                147 151

Chain C from PDB  Type:PROTEIN  Length:174
 aligned with NGAL_HUMAN | P80188 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:174
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193    
           NGAL_HUMAN    24 TSDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGCQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCID 197
               SCOP domains d3cmpc_ 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...eeeeeeeee.....hhhhhhhhhhhhhhh..hhh.ee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------LIPOCALIN     ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2d  PDB: C:4-26 Exon 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)
                 3cmp C   4 TSDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGSQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKAVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCID 177
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173

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

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

1a	d3cmpa_	A:
1b	d3cmpb_	B:
1c	d3cmpc_	C:

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

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

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.

Asymmetric Unit
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	Cis Peptide Bonds
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	NGAL_HUMAN \| P80188
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Related Entries Specified in the PDB File" available for 3CMP)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 20)

Sites (17, 17)

SS Bonds (3, 3)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 3)

Exons (6, 18)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

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