1J7E - JenaLib

Asym.Unit - manually (Jmol Viewer)

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)

Title :   A STRUCTURAL BASIS FOR THE UNIQUE BINDING FEATURES OF THE HUMAN VITAMIN D-BINDING PROTEIN

Authors :   C. Verboven, A. Rabijns, M. De Maeyer, H. Van Baelen, R. Bouillon, C. De Ranter

Date :   16 May 01 (Deposition) - 06 Feb 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.55

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

Keywords :   Vitamin D Binding, Vitamin D3 Analogue, Group-Specific Component, Gc-Globulin, Transport, Ligand Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Verboven, A. Rabijns, M. De Maeyer, H. Van Baelen, R. Bouillon, C. De Ranter
A Structural Basis For The Unique Binding Features Of The Human Vitamin D-Binding Protein.
Nat. Struct. Biol. V. 9 131 2002
PubMed-ID: 11799400 | Reference-DOI: 10.1038/NSB754
(for further references see the PDB file header)

Molecule 1 - VITAMIN D BINDING PROTEIN
	Chains	:	A, B
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	JY	2	Ligand/Ion	3-(2-{4-[2-(5-HYDROXY-2-METHYLENE-CYCLOHEXYLIDENE)-ETHYLIDENE]-7A-METHYL-OCTAHYDRO-INDEN-1-YL}-PROPYL)-PHENOL
2	OLA	3	Ligand/Ion	OLEIC ACID

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	JY	-1	Ligand/Ion	3-(2-{4-[2-(5-HYDROXY-2-METHYLENE-CYCLOHEXYLIDENE)-ETHYLIDENE]-7A-METHYL-OCTAHYDRO-INDEN-1-YL}-PROPYL)-PHENOL
2	OLA	1	Ligand/Ion	OLEIC ACID

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	JY	-1	Ligand/Ion	3-(2-{4-[2-(5-HYDROXY-2-METHYLENE-CYCLOHEXYLIDENE)-ETHYLIDENE]-7A-METHYL-OCTAHYDRO-INDEN-1-YL}-PROPYL)-PHENOL
2	OLA	2	Ligand/Ion	OLEIC ACID

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:8 , VAL A:12 , GLU A:15 , SER A:28 , LEU A:31 , TYR A:32 , LYS A:35 , LEU A:75 , SER A:76 , SER A:79 , MET A:107 , HOH A:521 , ASP B:364 , THR B:367	BINDING SITE FOR RESIDUE JY A 501
2	AC2	SOFTWARE	GLU B:8 , GLU B:15 , LEU B:27 , SER B:28 , TYR B:32 , PHE B:36 , LEU B:47 , TYR B:68 , SER B:76 , SER B:79 , MET B:107	BINDING SITE FOR RESIDUE JY B 502
3	AC3	SOFTWARE	VAL A:348 , GLU A:350 , PRO A:351 , LYS A:354 , GLU A:379 , PHE A:383 , ASP A:451	BINDING SITE FOR RESIDUE OLA A 502
4	AC4	SOFTWARE	GLU B:379	BINDING SITE FOR RESIDUE OLA B 503
5	AC5	SOFTWARE	ASP A:361 , ALA B:208 , ALA B:209 , TYR B:210 , LYS B:214 , LEU B:444	BINDING SITE FOR RESIDUE OLA B 504

Asymmetric Unit

No.	Residues
1	A:13	-	A:59
2	A:80	-	A:96
3	A:95	-	A:106
4	A:129	-	A:174
5	A:173	-	A:182
6	A:204	-	A:250
7	A:249	-	A:257
8	A:270	-	A:284
9	A:283	-	A:295
10	A:319	-	A:360
11	A:359	-	A:368
12	A:391	-	A:437
13	A:436	-	A:446
14	B:13	-	B:59
15	B:58	-	B:67
16	B:80	-	B:96
17	B:95	-	B:106
18	B:129	-	B:174
19	B:173	-	B:182
20	B:204	-	B:250
21	B:249	-	B:257
22	B:270	-	B:284
23	B:283	-	B:295
24	B:319	-	B:360
25	B:359	-	B:368
26	B:391	-	B:437
27	B:436	-	B:446

(no "Cis Peptide Bond" information available for 1J7E)

Asymmetric Unit (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_000548	D	432	E	VTDB_HUMAN	Polymorphism	7041	A/B	D	416	E
2	UniProt	VAR_000549	K	436	T	VTDB_HUMAN	Polymorphism	4588	A/B	T	420	T
3	UniProt	VAR_014120	R	445	C	VTDB_HUMAN	Polymorphism	---	A/B	R	429	C
4	UniProt	VAR_014121	R	445	H	VTDB_HUMAN	Polymorphism	9016	A/B	R	429	H

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

Biological Unit 1 (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_000548	D	432	E	VTDB_HUMAN	Polymorphism	7041	A	D	416	E
2	UniProt	VAR_000549	K	436	T	VTDB_HUMAN	Polymorphism	4588	A	T	420	T
3	UniProt	VAR_014120	R	445	C	VTDB_HUMAN	Polymorphism	---	A	R	429	C
4	UniProt	VAR_014121	R	445	H	VTDB_HUMAN	Polymorphism	9016	A	R	429	H

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

Biological Unit 2 (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_000548	D	432	E	VTDB_HUMAN	Polymorphism	7041	B	D	416	E
2	UniProt	VAR_000549	K	436	T	VTDB_HUMAN	Polymorphism	4588	B	T	420	T
3	UniProt	VAR_014120	R	445	C	VTDB_HUMAN	Polymorphism	---	B	R	429	C
4	UniProt	VAR_014121	R	445	H	VTDB_HUMAN	Polymorphism	9016	B	R	429	H

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALBUMIN_2	PS51438	Albumin domain profile.	VTDB_HUMAN	16-208 209-394	2	- A:193-378 B:193-378
2	ALBUMIN_1	PS00212	Albumin domain signature.	VTDB_HUMAN	182-206	2	A:166-190 B:166-190

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALBUMIN_2	PS51438	Albumin domain profile.	VTDB_HUMAN	16-208 209-394	1	- A:193-378 -
2	ALBUMIN_1	PS00212	Albumin domain signature.	VTDB_HUMAN	182-206	1	A:166-190 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALBUMIN_2	PS51438	Albumin domain profile.	VTDB_HUMAN	16-208 209-394	1	- - B:193-378
2	ALBUMIN_1	PS00212	Albumin domain signature.	VTDB_HUMAN	182-206	1	- B:166-190

Asymmetric Unit (12, 23)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.3a	ENST00000273951	3a	ENSE00001138631	chr4:72650079-72649678	402	VTDB_HUMAN	1-20	20	1	- B:3-4	- 2
1.4b	ENST00000273951	4b	ENSE00000969915	chr4:72635117-72635048	70	VTDB_HUMAN	20-43	24	2	A:7-27 B:4-27	21 24
1.5	ENST00000273951	5	ENSE00000969916	chr4:72634150-72634018	133	VTDB_HUMAN	43-87	45	2	A:27-71 (gaps) B:27-71	45 45
1.6b	ENST00000273951	6b	ENSE00000969917	chr4:72631360-72631149	212	VTDB_HUMAN	88-158	71	2	A:72-142 (gaps) B:72-142 (gaps)	71 71
1.7	ENST00000273951	7	ENSE00000969918	chr4:72629653-72629521	133	VTDB_HUMAN	158-202	45	2	A:142-186 B:142-186	45 45
1.8	ENST00000273951	8	ENSE00000969919	chr4:72629219-72629125	95	VTDB_HUMAN	203-234	32	2	A:187-218 B:187-218	32 32
1.9	ENST00000273951	9	ENSE00000969920	chr4:72623888-72623759	130	VTDB_HUMAN	234-277	44	2	A:218-261 B:218-261	44 44
1.10	ENST00000273951	10	ENSE00000969921	chr4:72622631-72622429	203	VTDB_HUMAN	278-345	68	2	A:262-329 B:262-329	68 68
1.11	ENST00000273951	11	ENSE00000969922	chr4:72620824-72620695	130	VTDB_HUMAN	345-388	44	2	A:329-372 B:329-372	44 44
1.12a	ENST00000273951	12a	ENSE00000969923	chr4:72620225-72620128	98	VTDB_HUMAN	389-421	33	2	A:373-405 B:373-405	33 33
1.13	ENST00000273951	13	ENSE00001138618	chr4:72618367-72618235	133	VTDB_HUMAN	421-465	45	2	A:405-449 B:405-449	45 45
1.14	ENST00000273951	14	ENSE00001178657	chr4:72611922-72611868	55	VTDB_HUMAN	466-474	9	2	A:450-457 B:450-456	8 7
1.15f	ENST00000273951	15f	ENSE00002022228	chr4:72607587-72607410	178	VTDB_HUMAN	-	0	0	-	-

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:435
 aligned with VTDB_HUMAN | P02774 from UniProtKB/Swiss-Prot  Length:474

    Alignment length:451
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472 
           VTDB_HUMAN    23 YEKNKVCKEFSHLGKEDFTSLSLVLYSRKFPSGTFEQVSQLVKEVVSLTEACCAEGADPDCYDTRTSALSAKSCESNSPFPVHPGTAECCTKEGLERKLCMAALKHQPQEFPTYVEPTNDEICEAFRKDPKEYANQFMWEYSTNYGQAPLSLLVSYTKSYLSMVGSCCTSASPTVCFLKERLQLKHLSLLTTLSNRVCSQYAAYGEKKSRLSNLIKLAQKVPTADLEDVLPLAEDITNILSKCCESASEDCMAKELPEHTVKLCDNLSTKNSKFEDCCQEKTAMDVFVCTYFMPAAQLPELPDVELPTNKDVCDPGNTKVMDKYTFELSRRTHLPEVFLSKVLEPTLKSLGECCDVEDSTTCFNAKGPLLKKELSSFIDKGQELCADYSENTFTEYKKKLAERLKAKLPDATPKELAKLVNKRSDFASNCCSINSPPLYCDSEIDAELKNI 473
               SCOP domains d1j7ea1 A:7-198 Vitamin D binding protein                                                                                                                                                       d1j7ea2 A:199-386 Vitamin D binding protein                                                                                                                                                 d1j7ea3 A:387-457 Vitamin D binding protein                             SCOP domains
               CATH domains 1j7eA01 A:7-111  [code=1.10.246.10, no name defined]                                                     ------------1j7eA02 A:124-211  [code=1.10.246.10, no name defined]                                  1j7eA03 A:212-299  [code=1.10.246.10, no name defined]                                  ---------------1j7eA04 A:315-391  [code=1.10.246.10, no name defined]                       ------1j7eA05 A:398-457  [code=1.10.246.10, no name defined]       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.---------..hhhhhhhhh.---.......hhhhhh..----...hhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..hhhhhhhh...hhhhhhhhhhhh...............hhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.. Sec.struct. author
             SAPs(SNPs) (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------E---T--------C---------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------H---------------------------- SAPs(SNPs) (2)
                PROSITE (1) ALBUMIN_2  PDB: - UniProt: 16-208                                                                                                                                                         ALBUMIN_2  PDB: A:193-378 UniProt: 209-394                                                                                                                                                ------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------ALBUMIN_1  PDB: A:166-190--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) --------------------Exon 1.5  PDB: A:27-71 (gaps) UniProt: 43-87 Exon 1.6b  PDB: A:72-142 (gaps) UniProt: 88-158                        --------------------------------------------Exon 1.8  PDB: A:187-218        -------------------------------------------Exon 1.10  PDB: A:262-329 UniProt: 278-345                          -------------------------------------------Exon 1.12a  PDB: A:373-405       --------------------------------------------1.14     Transcript 1 (1)
           Transcript 1 (2) Exon 1.4b  PDB: A:7-2------------------------------------------------------------------------------------------------------------------Exon 1.7  PDB: A:142-186 UniProt: 158-202    -------------------------------Exon 1.9  PDB: A:218-261 UniProt: 234-277   -------------------------------------------------------------------Exon 1.11  PDB: A:329-372 UniProt: 345-388  --------------------------------Exon 1.13  PDB: A:405-449 UniProt: 421-465   -------- Transcript 1 (2)
                 1j7e A   7 YEKNKVCKEFSHLGKEDFTSLSLVLYSRKFPSGTFEQVSQLVKEVVSLTEACC---------DTRTSALSAKSC---SPFPVHPGTAECCTK----RKLCMAALKHQPQEFPTYVEPTNDEICEAFRKDPKEYANQFMWEYSTNYGQAPLSLLVSYTKSYLSMVGSCCTSASPTVCFLKERLQLKHLSLLTTLSNRVCSQYAAYGEKKSRLSNLIKLAQKVPTADLEDVLPLAEDITNILSKCCESASEDCMAKELPEHTVKLCDNLSTKNSKFEDCCQEKTAMDVFVCTYFMPAAQLPELPDVELPTNKDVCDPGNTKVMDKYTFELSRRTHLPEVFLSKVLEPTLKSLGECCDVEDSTTCFNAKGPLLKKELSSFIDKGQELCADYSENTFTEYKKKLAERLKAKLPDATPTELAKLVNKRSDFASNCCSINSPPLYCDSEIDAELKNI 457
                                    16        26        36        46        56  |      -  |     76   |   |86        96 |    |106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456 
                                                                               59        69         80  84            98  103

Chain B from PDB  Type:PROTEIN  Length:447
 aligned with VTDB_HUMAN | P02774 from UniProtKB/Swiss-Prot  Length:474

    Alignment length:454
                                    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       418       428       438       448       458       468    
           VTDB_HUMAN    19 RGRDYEKNKVCKEFSHLGKEDFTSLSLVLYSRKFPSGTFEQVSQLVKEVVSLTEACCAEGADPDCYDTRTSALSAKSCESNSPFPVHPGTAECCTKEGLERKLCMAALKHQPQEFPTYVEPTNDEICEAFRKDPKEYANQFMWEYSTNYGQAPLSLLVSYTKSYLSMVGSCCTSASPTVCFLKERLQLKHLSLLTTLSNRVCSQYAAYGEKKSRLSNLIKLAQKVPTADLEDVLPLAEDITNILSKCCESASEDCMAKELPEHTVKLCDNLSTKNSKFEDCCQEKTAMDVFVCTYFMPAAQLPELPDVELPTNKDVCDPGNTKVMDKYTFELSRRTHLPEVFLSKVLEPTLKSLGECCDVEDSTTCFNAKGPLLKKELSSFIDKGQELCADYSENTFTEYKKKLAERLKAKLPDATPKELAKLVNKRSDFASNCCSINSPPLYCDSEIDAELKN 472
               SCOP domains d1j7eb1 B:3-198 Vitamin D binding protein                                                                                                                                                           d1j7eb2 B:199-386 Vitamin D binding protein                                                                                                                                                 d1j7eb3 B:387-456 Vitamin D binding protein                            SCOP domains
               CATH domains ----1j7eB01 B:7-111  [code=1.10.246.10, no name defined]                                                     ------------1j7eB02 B:124-211  [code=1.10.246.10, no name defined]                                  1j7eB03 B:212-299  [code=1.10.246.10, no name defined]                                  ---------------1j7eB04 B:315-391  [code=1.10.246.10, no name defined]                       ------1j7eB05 B:398-456  [code=1.10.246.10, no name defined]      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh............hhhhh.-------...................hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..hhhhhhhh...hhhhhhhhhhh................hhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh. Sec.struct. author
             SAPs(SNPs) (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------E---T--------C--------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------H--------------------------- SAPs(SNPs) (2)
                PROSITE (1) ALBUMIN_2  PDB: - UniProt: 16-208                                                                                                                                                             ALBUMIN_2  PDB: B:193-378 UniProt: 209-394                                                                                                                                                ------------------------------------------------------------------------------ PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------ALBUMIN_1  PDB: B:166-190-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.----------------------Exon 1.5  PDB: B:27-71 UniProt: 43-87        Exon 1.6b  PDB: B:72-142 (gaps) UniProt: 88-158                        --------------------------------------------Exon 1.8  PDB: B:187-218        -------------------------------------------Exon 1.10  PDB: B:262-329 UniProt: 278-345                          -------------------------------------------Exon 1.12a  PDB: B:373-405       --------------------------------------------1.14    Transcript 1 (1)
           Transcript 1 (2) -Exon 1.4b  PDB: B:4-27  ------------------------------------------------------------------------------------------------------------------Exon 1.7  PDB: B:142-186 UniProt: 158-202    -------------------------------Exon 1.9  PDB: B:218-261 UniProt: 234-277   -------------------------------------------------------------------Exon 1.11  PDB: B:329-372 UniProt: 345-388  --------------------------------Exon 1.13  PDB: B:405-449 UniProt: 421-465   ------- Transcript 1 (2)
                 1j7e B   3 RGRDYEKNKVCKEFSHLGKEDFTSLSLVLYSRKFPSGTFEQVSQLVKEVVSLTEACCAEGADPDCYDTRTSALSAKSCESNSPFPVHPGTAECCT-------LCMAALKHQPQEFPTYVEPTNDEICEAFRKDPKEYANQFMWEYSTNYGQAPLSLLVSYTKSYLSMVGSCCTSASPTVCFLKERLQLKHLSLLTTLSNRVCSQYAAYGEKKSRLSNLIKLAQKVPTADLEDVLPLAEDITNILSKCCESASEDCMAKELPEHTVKLCDNLSTKNSKFEDCCQEKTAMDVFVCTYFMPAAQLPELPDVELPTNKDVCDPGNTKVMDKYTFELSRRTHLPEVFLSKVLEPTLKSLGECCDVEDSTTCFNAKGPLLKKELSSFIDKGQELCADYSENTFTEYKKKLAERLKAKLPDATPTELAKLVNKRSDFASNCCSINSPPLYCDSEIDAELKN 456
                                    12        22        32        42        52        62        72        82        92    |    -  |    112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452    
                                                                                                                         97     105

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 alpha proteins (14657)

Fold: Serum albumin-like (99)

Superfamily: Serum albumin-like (99)

Family: Serum albumin-like (75)

Protein domain: Vitamin D binding protein (6)

Human (Homo sapiens) [TaxId: 9606] (6)

1a	d1j7ea1	A:7-198
1b	d1j7ea2	A:199-386
1c	d1j7ea3	A:387-457
1d	d1j7eb1	B:3-198
1e	d1j7eb2	B:199-386
1f	d1j7eb3	B:387-456

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Serum Albumin; Chain A, Domain 1 (74)

Homologous Superfamily: [code=1.10.246.10, no name defined] (60)

Human (Homo sapiens) (57)

1a	1j7eA02	A:124-211
1b	1j7eB02	B:124-211
1c	1j7eA03	A:212-299
1d	1j7eB03	B:212-299
1e	1j7eA01	A:7-111
1f	1j7eB01	B:7-111
1g	1j7eA04	A:315-391
1h	1j7eB04	B:315-391
1i	1j7eA05	A:398-457
1j	1j7eB05	B:398-456

(no "Pfam Domain" information available for 1J7E)

Asymmetric Unit(hide GO term definitions)

Chain A,B (VTDB_HUMAN | P02774)

molecular function
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
	GO:1902118	calcidiol binding	Interacting selectively and non-covalently with calcidiol.
	GO:0005499	vitamin D binding	Interacting selectively and non-covalently with vitamin D, any of a group of related, fat-soluble compounds that are derived from delta-5,7 steroids and play a central role in calcium metabolism. Specific forms of vitamin D include calciferol (ergocalciferol; vitamin D2) and cholecalciferol (calciol; vitamin D3).
	GO:0051183	vitamin transporter activity	Enables the directed movement of vitamins into, out of or within a cell, or between cells. A vitamin is one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body.
biological process
	GO:0007565	female pregnancy	The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
	GO:0007595	lactation	The regulated release of milk from the mammary glands and the period of time that a mother lactates to feed her young.
	GO:0032355	response to estradiol	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
	GO:0031667	response to nutrient levels	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of nutrients.
	GO:0048545	response to steroid hormone	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a steroid hormone stimulus.
	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.
	GO:0042359	vitamin D metabolic process	The chemical reactions and pathways involving vitamin D, any of a group of related, fat-soluble compounds that are derived from delta-5,7 steroids and play a central role in calcium metabolism. Specific forms of vitamin D include calciferol (ergocalciferol; vitamin D2) and cholecalciferol (calciol; vitamin D3).
	GO:0051180	vitamin transport	The directed movement of vitamins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A vitamin is one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body.
cellular component
	GO:0030424	axon	The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
	GO:0072562	blood microparticle	A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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.
	GO:0043202	lysosomal lumen	The volume enclosed within the lysosomal membrane.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.

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	VTDB_HUMAN \| P02774	:	1j78 1kw2 1kxp 1lot 1ma9

1j78	CRYSTALLOGRAPHIC ANALYSIS OF THE VITAMIN D BINDING PROTEIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (27, 27)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 8)

PROSITE Motifs (2, 4)

Exons (12, 23)

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SCOP Domains (1, 6)

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Gene Ontology (20, 20)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File