Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3VE1

The 2.9 angstrom crystal structure of Transferrin binding protein B (TbpB) from serogroup B M982 Neisseria meningitidis in complex with human transferrin

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005515	molecular_function	protein binding
A	0009279	cellular_component	cell outer membrane
A	0009986	cellular_component	cell surface
B	0005506	molecular_function	iron ion binding
B	0005515	molecular_function	protein binding
B	0005576	cellular_component	extracellular region
B	0005615	cellular_component	extracellular space
B	0005769	cellular_component	early endosome
B	0005770	cellular_component	late endosome
B	0005788	cellular_component	endoplasmic reticulum lumen
B	0005886	cellular_component	plasma membrane
B	0005905	cellular_component	clathrin-coated pit
B	0006811	biological_process	monoatomic ion transport
B	0006826	biological_process	iron ion transport
B	0006879	biological_process	intracellular iron ion homeostasis
B	0007166	biological_process	cell surface receptor signaling pathway
B	0008198	molecular_function	ferrous iron binding
B	0008199	molecular_function	ferric iron binding
B	0009925	cellular_component	basal plasma membrane
B	0009986	cellular_component	cell surface
B	0010008	cellular_component	endosome membrane
B	0016020	cellular_component	membrane
B	0016324	cellular_component	apical plasma membrane
B	0019731	biological_process	antibacterial humoral response
B	0019899	molecular_function	enzyme binding
B	0030139	cellular_component	endocytic vesicle
B	0030316	biological_process	osteoclast differentiation
B	0030669	cellular_component	clathrin-coated endocytic vesicle membrane
B	0031410	cellular_component	cytoplasmic vesicle
B	0031647	biological_process	regulation of protein stability
B	0031982	cellular_component	vesicle
B	0032436	biological_process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
B	0034774	cellular_component	secretory granule lumen
B	0034986	molecular_function	iron chaperone activity
B	0044325	molecular_function	transmembrane transporter binding
B	0045178	cellular_component	basal part of cell
B	0046872	molecular_function	metal ion binding
B	0048260	biological_process	positive regulation of receptor-mediated endocytosis
B	0048471	cellular_component	perinuclear region of cytoplasm
B	0055037	cellular_component	recycling endosome
B	0060586	biological_process	multicellular organismal-level iron ion homeostasis
B	0070062	cellular_component	extracellular exosome
B	0071281	biological_process	cellular response to iron ion
B	0072562	cellular_component	blood microparticle
B	1990459	molecular_function	transferrin receptor binding
B	1990712	cellular_component	HFE-transferrin receptor complex
C	0005515	molecular_function	protein binding
C	0009279	cellular_component	cell outer membrane
C	0009986	cellular_component	cell surface
D	0005506	molecular_function	iron ion binding
D	0005515	molecular_function	protein binding
D	0005576	cellular_component	extracellular region
D	0005615	cellular_component	extracellular space
D	0005769	cellular_component	early endosome
D	0005770	cellular_component	late endosome
D	0005788	cellular_component	endoplasmic reticulum lumen
D	0005886	cellular_component	plasma membrane
D	0005905	cellular_component	clathrin-coated pit
D	0006811	biological_process	monoatomic ion transport
D	0006826	biological_process	iron ion transport
D	0006879	biological_process	intracellular iron ion homeostasis
D	0007166	biological_process	cell surface receptor signaling pathway
D	0008198	molecular_function	ferrous iron binding
D	0008199	molecular_function	ferric iron binding
D	0009925	cellular_component	basal plasma membrane
D	0009986	cellular_component	cell surface
D	0010008	cellular_component	endosome membrane
D	0016020	cellular_component	membrane
D	0016324	cellular_component	apical plasma membrane
D	0019731	biological_process	antibacterial humoral response
D	0019899	molecular_function	enzyme binding
D	0030139	cellular_component	endocytic vesicle
D	0030316	biological_process	osteoclast differentiation
D	0030669	cellular_component	clathrin-coated endocytic vesicle membrane
D	0031410	cellular_component	cytoplasmic vesicle
D	0031647	biological_process	regulation of protein stability
D	0031982	cellular_component	vesicle
D	0032436	biological_process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
D	0034774	cellular_component	secretory granule lumen
D	0034986	molecular_function	iron chaperone activity
D	0044325	molecular_function	transmembrane transporter binding
D	0045178	cellular_component	basal part of cell
D	0046872	molecular_function	metal ion binding
D	0048260	biological_process	positive regulation of receptor-mediated endocytosis
D	0048471	cellular_component	perinuclear region of cytoplasm
D	0055037	cellular_component	recycling endosome
D	0060586	biological_process	multicellular organismal-level iron ion homeostasis
D	0070062	cellular_component	extracellular exosome
D	0071281	biological_process	cellular response to iron ion
D	0072562	cellular_component	blood microparticle
D	1990459	molecular_function	transferrin receptor binding
D	1990712	cellular_component	HFE-transferrin receptor complex

Functional Information from PDB Data

site_id	AC1
Number of Residues	1
Details	BINDING SITE FOR RESIDUE GOL A 701

Chain	Residue
B	PHE211

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL A 702

Chain	Residue
A	GLY286
A	GLU529
A	ARG530
A	HOH809

site_id	AC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE CO3 B 701

Chain	Residue
B	THR457
B	ALA458
B	GLY459
B	TYR517
B	HIS585
B	FE702
B	ASP392
B	TYR426
B	THR452
B	ARG456

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE B 702

Chain	Residue
B	ASP392
B	TYR426
B	TYR517
B	HIS585
B	CO3701

site_id	AC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL B 703

Chain	Residue
B	ASP63
B	ALA64
B	TYR95
B	SER125
B	PRO247
B	SER248
B	LYS296

site_id	AC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL B 704

Chain	Residue
B	TYR95
B	THR120
B	ARG124
B	SER125
B	ALA126
B	GLY127
B	TYR188

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL B 705

Chain	Residue
B	MET109
B	ASN110
B	LEU134
B	ASP138

site_id	AC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL B 706

Chain	Residue
B	CYS227
B	LEU228
B	ASP240
B	CYS241
B	HIS242

site_id	AC9
Number of Residues	2
Details	BINDING SITE FOR RESIDUE GOL B 707

Chain	Residue
B	GLU375
B	THR667

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL B 708

Chain	Residue
A	PRO122
B	GLY502
B	LEU503
B	ASN504

site_id	BC2
Number of Residues	11
Details	BINDING SITE FOR RESIDUE GOL C 701

Chain	Residue
C	GLY39
C	GLY40
C	TYR165
C	ARG288
C	SER316
C	GLY317
C	GLY318
C	PHE320
C	PHE400
C	HOH820
C	HOH824

site_id	BC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE CO3 D 701

Chain	Residue
D	ASP392
D	TYR426
D	THR452
D	ARG456
D	THR457
D	ALA458
D	GLY459
D	TYR517
D	HIS585
D	FE702

site_id	BC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE D 702

Chain	Residue
D	ASP392
D	TYR426
D	TYR517
D	HIS585
D	CO3701

site_id	BC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL D 703

Chain	Residue
D	TYR95
D	THR120
D	ARG124
D	SER125
D	ALA126
D	GLY127
D	TYR188

site_id	BC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL D 704

Chain	Residue
D	GLU375
D	GLY487
D	THR667
D	SER668

site_id	BC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL D 705

Chain	Residue
D	CYS227
D	LEU228
D	HIS242
D	GLU318

site_id	BC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL D 706

Chain	Residue
D	LEU134
D	ASP138
D	HOH855

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
B	TYR95-ASP104
B	TYR426-SER435

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

Chain	Residue	Details
B	TYR188-PHE204
B	TYR517-PHE532

site_id	PS00207
Number of Residues	31
Details	TRANSFERRIN_LIKE_3 Transferrin-like domain signature 3. QYeLLClDntrkp...VdeykdChlAqvpsHtVV

Chain	Residue	Details
B	GLN222-VAL252
B	ASP558-VAL588

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	104
Details	Region: {"description":"Disordered","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	18
Details	Compositional bias: {"description":"Basic and acidic residues","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	644
Details	Domain: {"description":"Transferrin-like 1","evidences":[{"source":"PROSITE-ProRule","id":"PRU00741","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	644
Details	Domain: {"description":"Transferrin-like 2","evidences":[{"source":"PROSITE-ProRule","id":"PRU00741","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"22327295","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3V83","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	8
Details	Binding site: {}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00741","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"22327295","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22343719","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"31636418","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3V83","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3VE1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6SOY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6SOZ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00741","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	2
Details	Modified residue: {"description":"Dimethylated arginine","evidences":[{"source":"UniProtKB","id":"P12346","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	4
Details	Modified residue: {"description":"Phosphoserine; by FAM20C","evidences":[{"source":"PubMed","id":"26091039","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	2
Details	Glycosylation: {"description":"O-linked (GalNAc...) serine","featureId":"CAR_000073"}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	2
Details	Glycosylation: {"description":"N-linked (GlcNAc...) (complex) asparagine","featureId":"CAR_000074","evidences":[{"source":"PubMed","id":"14760718","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15084671","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15536627","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16335952","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19159218","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19838169","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22327295","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"31636418","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"6SOY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6SOZ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	2
Details	Glycosylation: {"description":"N-linked (GlcNAc...) asparagine; atypical; partial","evidences":[{"source":"PubMed","id":"15536627","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	2
Details	Glycosylation: {"description":"N-linked (GlcNAc...) (complex) asparagine","featureId":"CAR_000075","evidences":[{"source":"PubMed","id":"14760718","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15084671","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15536627","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16335952","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16740002","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19139490","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19159218","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19838169","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22327295","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

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