Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1CB6

STRUCTURE OF HUMAN APOLACTOFERRIN AT 2.0 A RESOLUTION.

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0001503	biological_process	ossification
A	0001530	molecular_function	lipopolysaccharide binding
A	0001817	biological_process	regulation of cytokine production
A	0002227	biological_process	innate immune response in mucosa
A	0002376	biological_process	immune system process
A	0003677	molecular_function	DNA binding
A	0004252	molecular_function	serine-type endopeptidase activity
A	0004869	molecular_function	cysteine-type endopeptidase inhibitor activity
A	0005506	molecular_function	iron ion binding
A	0005515	molecular_function	protein binding
A	0005576	cellular_component	extracellular region
A	0005615	cellular_component	extracellular space
A	0005634	cellular_component	nucleus
A	0005737	cellular_component	cytoplasm
A	0005769	cellular_component	early endosome
A	0005886	cellular_component	plasma membrane
A	0006508	biological_process	proteolysis
A	0006811	biological_process	monoatomic ion transport
A	0006826	biological_process	iron ion transport
A	0006959	biological_process	humoral immune response
A	0008201	molecular_function	heparin binding
A	0008233	molecular_function	peptidase activity
A	0008236	molecular_function	serine-type peptidase activity
A	0009986	cellular_component	cell surface
A	0016787	molecular_function	hydrolase activity
A	0019731	biological_process	antibacterial humoral response
A	0019732	biological_process	antifungal humoral response
A	0030141	cellular_component	secretory granule
A	0031640	biological_process	killing of cells of another organism
A	0031665	biological_process	negative regulation of lipopolysaccharide-mediated signaling pathway
A	0032680	biological_process	regulation of tumor necrosis factor production
A	0032780	biological_process	negative regulation of ATP-dependent activity
A	0032991	cellular_component	protein-containing complex
A	0033690	biological_process	positive regulation of osteoblast proliferation
A	0034145	biological_process	positive regulation of toll-like receptor 4 signaling pathway
A	0035580	cellular_component	specific granule lumen
A	0042581	cellular_component	specific granule
A	0042742	biological_process	defense response to bacterium
A	0043066	biological_process	negative regulation of apoptotic process
A	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
A	0043539	molecular_function	protein serine/threonine kinase activator activity
A	0044793	biological_process	negative regulation by host of viral process
A	0045071	biological_process	negative regulation of viral genome replication
A	0045669	biological_process	positive regulation of osteoblast differentiation
A	0046872	molecular_function	metal ion binding
A	0048525	biological_process	negative regulation of viral process
A	0050829	biological_process	defense response to Gram-negative bacterium
A	0051092	biological_process	positive regulation of NF-kappaB transcription factor activity
A	0055037	cellular_component	recycling endosome
A	0060349	biological_process	bone morphogenesis
A	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
A	0070062	cellular_component	extracellular exosome
A	0071902	biological_process	positive regulation of protein serine/threonine kinase activity
A	0097013	cellular_component	phagocytic vesicle lumen
A	0140912	molecular_function	membrane destabilizing activity
A	1900159	biological_process	positive regulation of bone mineralization involved in bone maturation
A	1900229	biological_process	negative regulation of single-species biofilm formation in or on host organism
A	1902732	biological_process	positive regulation of chondrocyte proliferation
A	1904724	cellular_component	tertiary granule lumen
A	2000308	biological_process	negative regulation of tumor necrosis factor (ligand) superfamily member 11 production
A	2001205	biological_process	negative regulation of osteoclast development

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CL A 1701

Chain	Residue
A	ARG1121
A	ALA1123
A	GLY1124
A	TYR1192
A	THR1117

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CL A 1702

Chain	Residue
A	THR1461
A	ARG1465
A	GLY1468
A	TYR1528
A	HOH2237

site_id	CLA
Number of Residues	4
Details	CHLORIDE ION LOCATED NEAR CARBONATE SITE IN CLOSED C LOBE, FORMING HYDROGEN BONDS WITH THR461_OG1, ARG465_NE, ARG465_NH2, GLY468_N AND TYR528_OH

Chain	Residue
A	THR1461
A	ARG1465
A	GLY1468
A	TYR1528

site_id	CLB
Number of Residues	4
Details	CHLORIDE ION LOCATED NEAR CARBONATE SITE IN OPEN N LOBE, FORMING HYDROGEN BONDS WITH THR117_OG1, ARG121_NE, ALA123_N AND TYR192_OH

Chain	Residue
A	THR1117
A	ARG1121
A	ALA1123
A	TYR1192

Functional Information from PROSITE/UniProt

site_id	PS00205
Number of Residues	10
Details	TRANSFERRIN_LIKE_1 Transferrin-like domain signature 1. YyAVAVVKKG

Chain	Residue	Details
A	TYR1092-GLY1101
A	TYR1435-SER1444

site_id	PS00206
Number of Residues	17
Details	TRANSFERRIN_LIKE_2 Transferrin-like domain signature 2. YsGAFKCLrdgaGDVAF

Chain	Residue	Details
A	TYR1192-PHE1208
A	TYR1528-PHE1544

site_id	PS00207
Number of Residues	31
Details	TRANSFERRIN_LIKE_3 Transferrin-like domain signature 3. EYeLLCpDntrkp...VdkfkdChlArvpsHaVV

Chain	Residue	Details
A	GLU1226-VAL1256
A	ASP1570-VAL1600

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	47
Details	Peptide: {"description":"Lactoferricin-H","featureId":"PRO_0000422770"}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	30
Details	Peptide: {"description":"Kaliocin-1","featureId":"PRO_0000035733"}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	5
Details	Peptide: {"description":"Lactoferroxin-A","featureId":"PRO_0000035734"}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	4
Details	Peptide: {"description":"Lactoferroxin-B","featureId":"PRO_0000035735"}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	6
Details	Peptide: {"description":"Lactoferroxin-C","featureId":"PRO_0000035736"}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	327
Details	Domain: {"description":"Transferrin-like 1","evidences":[{"source":"PROSITE-ProRule","id":"PRU00741","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	331
Details	Domain: {"description":"Transferrin-like 2","evidences":[{"source":"PROSITE-ProRule","id":"PRU00741","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	9
Details	Region: {"description":"Bactericidal and antifungal activity"}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	4
Details	Region: {"description":"Critical for glycosaminoglycan, lipid A, lysozyme and DNA binding"}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	1
Details	Region: {"description":"Important for full bactericidal and antifungal activities"}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	10
Details	Region: {"description":"Interaction with lipopolysaccharide"}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	8
Details	Region: {"description":"Interaction with PspA"}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	5
Details	Region: {"description":"Involved in glycosaminoglycan binding"}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	1
Details	Active site: {"evidences":[{"source":"PubMed","id":"12535064","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	1
Details	Active site: {"description":"Nucleophile","evidences":[{"source":"PubMed","id":"12535064","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI16
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00741","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"10089347","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"10828980","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12450380","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15299793","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16201406","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17543335","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22900286","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8371268","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8594202","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8703903","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8931543","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9003186","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAR-2004","submissionDatabase":"PDB data bank","title":"Structure of human diferric lactoferrin at 2.5A resolution using crystals grown at pH 6.5.","authors":["Vikram P.","Prem Kumar R.","Singh N.","Kumar J.","Ethayathulla A.S.","Sharma S.","Kaur P.","Singh T.P."]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI17
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00741","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"10089347","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"10828980","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11128996","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12450380","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15299793","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"1581307","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16201406","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17543335","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22900286","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8371268","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8594202","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8931543","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9003186","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAR-2004","submissionDatabase":"PDB data bank","title":"Structure of human diferric lactoferrin at 2.5A resolution using crystals grown at pH 6.5.","authors":["Vikram P.","Prem Kumar R.","Singh N.","Kumar J.","Ethayathulla A.S.","Sharma S.","Kaur P.","Singh T.P."]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI18
Number of Residues	2
Details	Site: {"description":"Interaction with PspA"}

Chain

Residue

Details

site_id	SWS_FT_FI19
Number of Residues	1
Details	Site: {"description":"Important for iron binding"}

Chain

Residue

Details

site_id	SWS_FT_FI20
Number of Residues	1
Details	Glycosylation: {"description":"N-linked (GlcNAc...) asparagine","evidences":[{"source":"PubMed","id":"15299444","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15299793","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"1581307","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16201406","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18780401","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8069634","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAR-2004","submissionDatabase":"PDB data bank","title":"Structure of human diferric lactoferrin at 2.5A resolution using crystals grown at pH 6.5.","authors":["Vikram P.","Prem Kumar R.","Singh N.","Kumar J.","Ethayathulla A.S.","Sharma S.","Kaur P.","Singh T.P."]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI21
Number of Residues	1
Details	Glycosylation: {"description":"N-linked (GlcNAc...) asparagine","evidences":[{"source":"PubMed","id":"15299793","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"1581307","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16201406","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18780401","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19159218","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAR-2004","submissionDatabase":"PDB data bank","title":"Structure of human diferric lactoferrin at 2.5A resolution using crystals grown at pH 6.5.","authors":["Vikram P.","Prem Kumar R.","Singh N.","Kumar J.","Ethayathulla A.S.","Sharma S.","Kaur P.","Singh T.P."]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI22
Number of Residues	1
Details	Glycosylation: {"description":"N-linked (GlcNAc...) asparagine","evidences":[{"source":"PubMed","id":"18780401","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI23
Number of Residues	3
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"20404350","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)