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Theoretical Model (Jmol Viewer)

Title :   COMPARATIVE MODEL OF HUMAN INTRINSIC FACTOR IN COMPLEX WITH AQUO-COBALAMIN

Authors :   J. Wuerges, S. Geremia, L. Randaccio

Date :   21 Apr 06 (Deposition) - 13 Feb 07 (Release) - 13 Feb 07 (Revision)

Method :   THEORETICAL MODEL

Resolution :   NOT APPLICABLE

Chains :   Theor. Model : W^#,X
( ^#: chains that contain no standard or modified protein/DNA/RNA residue)

Keywords :   Ion Transport, Disease Mutation, Cobalt Transport, Comparative Model, Vitamin B12 Transport Protein, Cobalt, Transport, Polymorphism, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Wuerges, S. Geremia, L. Randaccio
Structural Study On Ligand Specificity Of Human Vitamin B12 Transporters.
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - GASTRIC INTRINSIC FACTOR
	Chains	:	X
	Engineered	:	YES
	Other Details	:	PROTEIN IN COMPLEX WITH H2O-COBALAMIN
	Synonym	:	INTRINSIC FACTOR, IF, INF
	Synthetic	:	YES


Theoretical Model	:

( ^#: chains that contain no standard or modified protein/DNA/RNA residue)

Summary Information (see also Sequences/Alignments below)

Theoretical Model (1, 1)

No.	Name	Count	Type	Full Name
1	B12	1	Ligand/Ion	COBALAMIN

(no "Site" information available for 2CKT)

Theoretical Model

No.	Residues
1	X:8	-	X:228
2	X:85	-	X:270
3	X:125	-	X:164

(no "Cis Peptide Bond" information available for 2CKT)

Theoretical Model (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_022742	Q	23	R	IF_HUMAN	Polymorphism	35211634	X	Q	5	R
2	UniProt	VAR_022743	S	46	L	IF_HUMAN	Disease (IFD)	121434322	X	S	28	L
3	UniProt	VAR_048753	G	65	R	IF_HUMAN	Polymorphism	11825834	X	G	47	R
4	UniProt	VAR_022744	N	255	S	IF_HUMAN	Polymorphism	35867471	X	N	237	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Theoretical Model (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COBALAMIN_BINDING	PS00468	Eukaryotic cobalamin-binding proteins signature.	IF_HUMAN	169-182	1	X:151-164

Theoretical Model (9, 9)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000257248	1a	ENSE00001170003	chr11:59612974-59612848	127	IF_HUMAN	1-27	27	1	X:1-9	9
1.2	ENST00000257248	2	ENSE00000916274	chr11:59611528-59611352	177	IF_HUMAN	27-86	60	1	X:9-68	60
1.3a	ENST00000257248	3a	ENSE00000916273	chr11:59610614-59610501	114	IF_HUMAN	86-124	39	1	X:68-106	39
1.3c	ENST00000257248	3c	ENSE00000916272	chr11:59610056-59609916	141	IF_HUMAN	124-171	48	1	X:106-153	48
1.4a	ENST00000257248	4a	ENSE00000916271	chr11:59608797-59608616	182	IF_HUMAN	171-231	61	1	X:153-213	61
1.5	ENST00000257248	5	ENSE00000916270	chr11:59604824-59604647	178	IF_HUMAN	232-291	60	1	X:214-273	60
1.6a	ENST00000257248	6a	ENSE00000916269	chr11:59603482-59603281	202	IF_HUMAN	291-358	68	1	X:273-340	68
1.7a	ENST00000257248	7a	ENSE00000916268	chr11:59599269-59599151	119	IF_HUMAN	358-398	41	1	X:340-380	41
1.8b	ENST00000257248	8b	ENSE00002164105	chr11:59597018-59596741	278	IF_HUMAN	398-417	20	1	X:380-399	20

Theoretical Model

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 X from PDB  Type:PROTEIN  Length:399
 aligned with IF_HUMAN | P27352 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:399
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408         
             IF_HUMAN    19 STQTQSSCSVPSAQEPLVNGIQVLMENSVTSSAYPNPSILIAMNLAGAYNLKAQKLLTYQLMSSDNNDLTIGQLGLTIMALTSSCRDPGDKVSILQRQMENWAPSSPNAEASAFYGPSLAILALCQKNSEATLPIAVRFAKTLLANSSPFNVDTGAMATLALTCMYNKIPVGSEEGYRSLFGQVLKDIVEKISMKIKDNGIIGDIYSTGLAMQALSVTPEPSKKEWNCKKTTDMILNEIKQGKFHNPMSIAQILPSLKGKTYLDVPQVTCSPDHEVQPTLPSNPGPGPTSASNITVIYTINNQLRGVELLFNETINVSVKSGSVLLVVLEEAQRKNPMFKFETTMTSWGLVVSSINNIAENVNHKTYWQFLSGVTPLNEGVADYIPFNHEHITANFTQY 417
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhh.........hhhhhhhh......hhhhhhhhhhh......hhhhhhhhhhhhhhh.......hhhhhhhhhhhh..........hhhhhhhhhhhhhhh.......hhhhhhhh......hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh..hhhhhhhh.......................eeeeeeeeee.............eeeeeee...hhhhhh.........eeeeeee..eeeeeeee.eee....eeeeeeeee.eee............eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----R----------------------L------------------R---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------COBALAMIN_BIND------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a----------------------------------------------------------Exon 1.3a  PDB: X:68-106               ----------------------------------------------Exon 1.4a  PDB: X:153-213 UniProt: 171-231                   Exon 1.5  PDB: X:214-273 UniProt: 232-291                   ------------------------------------------------------------------Exon 1.7a  PDB: X:340-380                ------------------- Transcript 1 (1)
           Transcript 1 (2) --------Exon 1.2  PDB: X:9-68 UniProt: 27-86                        -------------------------------------Exon 1.3c  PDB: X:106-153 UniProt: 124-171      -----------------------------------------------------------------------------------------------------------------------Exon 1.6a  PDB: X:273-340 UniProt: 291-358                          ---------------------------------------Exon 1.8b            Transcript 1 (2)
                 2ckt X   1 STQTQSSCSVPSAQEPLVNGIQVLMENSVTSSAYPNPSILIAMNLAGAYNLKAQKLLTYQLMSSDNNDLTIGHLGLTIMALTSSCRDPGDKVSILQRQMENWAPSSPNAEASAFYGPSLAILALCQKNSEATLPIAVRFAKTLLANSSPFNVDTGAMATLALTCMYNKIPVGSEEGYRSLFGQVLKDIVEKISMKIKDNGIIGDIYSTGLAMQALSVTPEPSKKEWNCKKTTDMILNEIKQGKFHNPMSIAQILPSLKGKTYLDVPQVTCSPDHEVQPTLPSNPGPGPTSASNITVIYTINNQLRGVELLFNETINVSVKSGSVLLVVLEEAQRKNPMFKFETTMTSWGLVVSSINNIAENVNHKTYWQFLSGVTPLNEGVADYIPFNHEHITANFTQY 399
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390

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 '\|'

(no "SCOP Domain" information available for 2CKT)

(no "CATH Domain" information available for 2CKT)

(no "Pfam Domain" information available for 2CKT)

Theoretical Model(hide GO term definitions)

Chain X (IF_HUMAN | P27352)

molecular function
	GO:0031419	cobalamin binding	Interacting selectively and non-covalently with cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
biological process
	GO:0009235	cobalamin metabolic process	The chemical reactions and pathways involving cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
	GO:0015889	cobalamin transport	The directed movement of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006824	cobalt ion transport	The directed movement of cobalt (Co) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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: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:0016324	apical plasma membrane	The region of the plasma membrane located at the apical end of the cell.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	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.
	GO:0043202	lysosomal lumen	The volume enclosed within the lysosomal membrane.
	GO:0005902	microvillus	Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells.

Theoretical Model
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(no "Sites" information available for 2ckt)

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(no "Related Entries Specified in the PDB File" available for 2CKT)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (0, 0)

SS Bonds (3, 3)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 4)

PROSITE Motifs (1, 1)

Exons (9, 9)

Sequences/Alignments

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SCOP Domains (0, 0)

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Gene Ontology (12, 12)

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