4HBQ - 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 A LOOP DELETED MUTANT OF HUMAN MADCAM-1 D1D2

Authors :   T. Springer, Y. Yu, J. Zhu

Date :   28 Sep 12 (Deposition) - 23 Jan 13 (Release) - 23 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

Keywords :   Immunoglobulin Superfamily, Integrin Alpha4Beta7, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Springer, Y. Yu, J. Zhu, J. -H. Wang, P. -S. Huang
A Different Fold With An Integrin-Binding Loop Specialized For Flexibility In Mucosal Addressin Cell Adhesion Molecule-1
To Be Published
PubMed: search

Molecule 1 - MUCOSAL ADDRESSIN CELL ADHESION MOLECULE 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Common	:	HUMAN
	Expression System Organ	:	KIDNEY
	Expression System Strain	:	HEK 293 GNTI(-)
	Expression System Taxid	:	9606
	Gene	:	MADCAM1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MADCAM-1, HMADCAM-1

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	NAG	-1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (3, 4)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:79 , HOH A:606 , HOH A:620 , HOH A:648 , ARG B:79 , ARG B:196	BINDING SITE FOR RESIDUE SO4 A 301
2	AC2	SOFTWARE	HOH A:600 , HOH A:611 , HOH A:656 , VAL B:1 , LEU B:188 , GLY B:190 , HOH B:577	BINDING SITE FOR RESIDUE GOL A 302
3	AC3	SOFTWARE	TYR A:208 , HOH A:555 , THR B:69 , GLY B:138 , GLN B:140 , ARG B:168 , HOH B:599	BINDING SITE FOR RESIDUE SO4 B 301
4	AC4	SOFTWARE	ILE A:151 , GLY A:152 , HOH A:554 , ASN B:61 , HOH B:458 , HOH B:555 , HOH B:563 , HOH B:587 , HOH B:594	BINDING SITE FOR RESIDUE NAG B 2061

Asymmetric Unit

No.	Residues
1	A:25	-	A:72
2	A:29	-	A:76
3	A:112	-	A:182
4	B:25	-	B:72
5	B:29	-	B:76
6	B:112	-	B:182

Asymmetric Unit

No.	Residues
1	Glu A:7	-	Pro A:8
2	Ser A:99	-	Pro A:100
3	Thr A:118	-	Pro A:119
4	Thr A:174	-	Pro A:175
5	Glu B:7	-	Pro B:8
6	Ser B:99	-	Pro B:100
7	Thr B:118	-	Pro B:119
8	Thr B:174	-	Pro B:175

(no "SAP(SNP)/Variant" information available for 4HBQ)

(no "PROSITE Motif" information available for 4HBQ)

(no "Exon" information available for 4HBQ)

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:206
                                                                                                                                                                                                                                              
               SCOP domains d4hbqa1 A:1-90 automated matches                                                          d4hbqa2 A:91-210 automated matches                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....eeeee....eeeeeee.......eeeee.......eeeee..eeeeee...hhhhheeeeeeeee..eeeeeeeeeeee....eeeee.........eeeeeeeee.......eeeeeee..ee....ee...eeeeeee..eeeeeeeeeee..........eeeeeeeeee..eeeeeeeeee....hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hbq A   1 VKPLQVEPPEPVVAVALGASRQLTCRLACADRGASVQWRGLDTSLGAVQSDTGRSVLTVRNASLSAAGTRVCVGSCGGRTFQHTVQLLVYAFPNQLTVSPAALVPGDPEVACTAHKVTPVDPNALSFSLLVGGQELEGAQALGPEVQQEPIGGDVLFRVTERWRLPPLGTPVPPALYCQATMRLPGLELSHRQAIPVLGGENLYFQ 210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  ||   164       174       184       194       204      
                                                                                                                                                                                  153|                                                    
                                                                                                                                                                                   158

Chain B from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                              
               SCOP domains d4hbqb1 B:1-90 automated matches                                                          d4hbqb2 B:91-210 automated matches                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....eeeee....eeeeeee.......eeeee.......eeee...eeeeee...hhhhheeeeeeeee..eeeeeeeeeeee....eeeee.........eeeeeeeee.......eeeeeee..ee....ee...eeeeeee..eeeeeeeeeee..........eeeeeeeeee..eeeeeeeeee....hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hbq B   1 VKPLQVEPPEPVVAVALGASRQLTCRLACADRGASVQWRGLDTSLGAVQSDTGRSVLTVRNASLSAAGTRVCVGSCGGRTFQHTVQLLVYAFPNQLTVSPAALVPGDPEVACTAHKVTPVDPNALSFSLLVGGQELEGAQALGPEVQQEPIGGDVLFRVTERWRLPPLGTPVPPALYCQATMRLPGLELSHRQAIPVLGGENLYFQ 210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  ||   164       174       184       194       204      
                                                                                                                                                                                  153|                                                    
                                                                                                                                                                                   158

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: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: automated matches (864)

Protein domain: automated matches (864)

Human (Homo sapiens) [TaxId: 9606] (448)

1a	d4hbqa1	A:1-90
1b	d4hbqb1	B:1-90

Family: I set domains (152)

Protein domain: automated matches (23)

Human (Homo sapiens) [TaxId: 9606] (22)

2a	d4hbqa2	A:91-210
2b	d4hbqb2	B:91-210

(no "CATH Domain" information available for 4HBQ)

(no "Pfam Domain" information available for 4HBQ)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Glu A:7 - Pro A:8	[ RasMol ]
		Glu B:7 - Pro B:8	[ RasMol ]
		Ser A:99 - Pro A:100	[ RasMol ]
		Ser B:99 - Pro B:100	[ RasMol ]
		Thr A:118 - Pro A:119	[ RasMol ]
		Thr A:174 - Pro A:175	[ RasMol ]
		Thr B:118 - Pro B:119	[ RasMol ]
		Thr B:174 - Pro B:175	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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	4hbq
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	MADCA_HUMAN \| Q13477
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	MADCA_HUMAN \| Q13477	:	1bqs 1gsm 4hc1 4hcr 4hd9

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

SS Bonds (6, 6)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (2, 4)

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Gene Ontology (16, 16)

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