3G5C - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURAL AND BIOCHEMICAL STUDIES ON THE ECTODOMAIN OF HUMAN ADAM22

Authors :   H. Liu, A. Shim, X. Chen, X. He

Date :   04 Feb 09 (Deposition) - 18 Aug 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.36

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

Keywords :   Alpha/Beta Fold, Cross-Linked Domain, Cell Adhesion, Cleavage On Pair Of Basic Residues, Egf-Like Domain, Glycoprotein, Membrane, Phosphoprotein, Transmembrane, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Liu, A. Shim, X. Chen, X. He
Structural And Biochemical Studies On The Ectodomain Of Human Adam22
J. Biol. Chem. 2009
PubMed: search

Molecule 1 - ADAM 22
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Plasmid	:	PACGP67A
	Expression System Taxid	:	7111
	Expression System Vector	:	PLASMID
	Fragment	:	M, D, C AND E DOMAINS
	Gene	:	ADAM22, MDC2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	A DISINTEGRIN AND METALLOPROTEINASE DOMAIN 22, METALLOPROTEINASE-LIKE, DISINTEGRIN-LIKE, AND CYSTEINE-RICH PROTEIN 2, METALLOPROTEINASE-DISINTEGRIN ADAM22-3

		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, 12)

No.	Name	Count	Type	Full Name
1	CA	6	Ligand/Ion	CALCIUM ION
2	NAG	6	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	MET A:499 , SER A:517 , ASN A:519 , GLU A:684	BINDING SITE FOR RESIDUE NAG A 1
02	AC2	SOFTWARE	HOH A:66 , THR A:606 , ASN A:607 , ILE A:608 , ASN A:634 , SER A:636 , GLU B:505	BINDING SITE FOR RESIDUE NAG A 2
03	AC3	SOFTWARE	HOH A:178 , LEU A:664 , SER A:673 , ASN A:675 , HOH A:805 , ARG B:317	BINDING SITE FOR RESIDUE NAG A 3
04	AC4	SOFTWARE	GLU A:242 , ASP A:325 , CYS A:433 , ASN A:436 , HOH A:776 , HOH A:800	BINDING SITE FOR RESIDUE CA A 801
05	AC5	SOFTWARE	GLU A:446 , CYS A:447 , GLY A:448 , ASN A:449 , PHE A:451 , GLU A:453 , GLU A:456 , ASP A:459	BINDING SITE FOR RESIDUE CA A 802
06	AC6	SOFTWARE	HOH A:109 , ASP A:511 , ILE A:512 , GLU A:514 , ASN A:526 , ILE A:527	BINDING SITE FOR RESIDUE CA A 803
07	AC7	SOFTWARE	SER B:517 , ASN B:519 , GLU B:684	BINDING SITE FOR RESIDUE NAG B 1
08	AC8	SOFTWARE	GLU A:505 , ASN B:607 , ILE B:608 , ASN B:634 , SER B:636	BINDING SITE FOR RESIDUE NAG B 2
09	AC9	SOFTWARE	ARG A:317 , LEU B:664 , SER B:673 , ASN B:675	BINDING SITE FOR RESIDUE NAG B 3
10	BC1	SOFTWARE	HOH B:122 , GLU B:242 , ASP B:325 , CYS B:433 , ASN B:436 , HOH B:778	BINDING SITE FOR RESIDUE CA B 801
11	BC2	SOFTWARE	GLU B:446 , CYS B:447 , GLY B:448 , ASN B:449 , PHE B:451 , GLU B:453 , GLU B:456 , ASP B:459	BINDING SITE FOR RESIDUE CA B 802
12	BC3	SOFTWARE	HOH B:82 , ASP B:511 , ILE B:512 , GLU B:514 , ASN B:526 , ILE B:527	BINDING SITE FOR RESIDUE CA B 803

Asymmetric Unit

No.	Residues
1	A:349	-	A:433
2	A:392	-	A:417
3	A:394	-	A:401
4	A:447	-	A:477
5	A:458	-	A:474
6	A:460	-	A:466
7	A:473	-	A:494
8	A:485	-	A:491
9	A:490	-	A:516
10	A:503	-	A:523
11	A:510	-	A:542
12	A:535	-	A:547
13	A:554	-	A:605
14	A:569	-	A:635
15	A:583	-	A:593
16	A:600	-	A:663
17	A:657	-	A:668
18	A:679	-	A:694
19	A:688	-	A:700
20	A:702	-	A:711
21	B:349	-	B:433
22	B:392	-	B:417
23	B:394	-	B:401
24	B:447	-	B:477
25	B:458	-	B:474
26	B:460	-	B:466
27	B:473	-	B:494
28	B:485	-	B:491
29	B:490	-	B:516
30	B:503	-	B:523
31	B:510	-	B:542
32	B:535	-	B:547
33	B:554	-	B:605
34	B:569	-	B:635
35	B:583	-	B:593
36	B:600	-	B:663
37	B:657	-	B:668
38	B:679	-	B:694
39	B:688	-	B:700
40	B:702	-	B:711

(no "Cis Peptide Bond" information available for 3G5C)

(no "SAP(SNP)/Variant" information available for 3G5C)

Asymmetric Unit (4, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADAM_MEPRO	PS50215	ADAM type metalloprotease domain profile.	ADA22_HUMAN	239-438	2	A:239-438 B:239-438
2	DISINTEGRIN_2	PS50214	Disintegrin domain profile.	ADA22_HUMAN	444-531	2	A:444-531 B:444-531
3	DISINTEGRIN_1	PS00427	Disintegrins signature.	ADA22_HUMAN	485-504	2	A:485-504 B:485-504
4	EGF_1	PS00022	EGF-like domain signature 1.	ADA22_HUMAN	700-711	2	A:700-711 B:700-711

Biological Unit 1 (4, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADAM_MEPRO	PS50215	ADAM type metalloprotease domain profile.	ADA22_HUMAN	239-438	1	A:239-438 -
2	DISINTEGRIN_2	PS50214	Disintegrin domain profile.	ADA22_HUMAN	444-531	1	A:444-531 -
3	DISINTEGRIN_1	PS00427	Disintegrins signature.	ADA22_HUMAN	485-504	1	A:485-504 -
4	EGF_1	PS00022	EGF-like domain signature 1.	ADA22_HUMAN	700-711	1	A:700-711 -

Biological Unit 2 (4, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADAM_MEPRO	PS50215	ADAM type metalloprotease domain profile.	ADA22_HUMAN	239-438	1	- B:239-438
2	DISINTEGRIN_2	PS50214	Disintegrin domain profile.	ADA22_HUMAN	444-531	1	- B:444-531
3	DISINTEGRIN_1	PS00427	Disintegrins signature.	ADA22_HUMAN	485-504	1	- B:485-504
4	EGF_1	PS00022	EGF-like domain signature 1.	ADA22_HUMAN	700-711	1	- B:700-711

(no "Exon" information available for 3G5C)

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:486
 aligned with ADA22_HUMAN | Q9P0K1 from UniProtKB/Swiss-Prot  Length:906

    Alignment length:486
                                   242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712      
          ADA22_HUMAN   233 NVEEETKYIELMIVNDHLMFKKHRLSVVHTNTYAKSVVNMADLIYKDQLKTRIVLVAMETWATDNKFAISENPLITLREFMKYRRDFIKEKSDAVHLFSGSQFESSRSGAAYIGGICSLLKGGGVNEFGKTDLMAVTLAQSLAHNIGIISDKRKLASGECKCEDTWSGCIMGDTGYYLPKKFTQCNIEEYHDFLNSGGGACLFNKPSKLLDPPECGNGFIETGEECDCGTPAECVLEGAECCKKCTLTQDSQCSDGLCCKKCKFQPMGTVCREAVNDCDIRETCSGNSSQCAPNIHKMDGYSCDGVQGICFGGRCKTRDRQCKYIWGQKVTASDKYCYEKLNIEGTEKGNCGKDKDTWIQCNKRDVLCGYLLCTNIGNIPRLGELDGEITSTLVVQQGRTLNCSGGHVKLEEDVDLGYVEDGTPCGPQMMCLEHRCLPVASFNFSTCLSSKEGTICSGNGVCSNELKCVCNRHWIGSDCNTYFPHN 718
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3g5cA02 A:463-517 Echistatin                           --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeeehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeee...........hhhhhhhhhhhhhhhh......eeeeee.........eee...........eeeee..hhhhhhhhhhhhhhhhhh...hhhhhhhh........................hhhhhhhhhhhhhh..hhhhhh.........................hhhhhh......ee..ee......................eee.........ee..................ee....eeee..eeehhhhhhhhhhh......hhhhhhhhh...................hhhhh.................ee....eeeeeee..eeeeeee..ee.....ee.......eee..eee....eee.hhhh...........hhhh.eee.....eee...ee.....ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ------ADAM_MEPRO  PDB: A:239-438 UniProt: 239-438                                                                                                                                                             -----DISINTEGRIN_2  PDB: A:444-531 UniProt: 444-531                                          ------------------------------------------------------------------------------------------------------------------------------------------------------------------------EGF_1       ------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DISINTEGRIN_1       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3g5c A 233 NVEEETKYIELMIVNDHLMFKKHRLSVVHTNTYAKSVVNMADLIYKDQLKTRIVLVAMETWATDNKFAISENPLITLREFMKYRRDFIKEKSDAVHLFSGSQFESSRSGAAYIGGICSLLKGGGVNEFGKTDLMAVTLAQSLAHNIGIISDKRKLASGECKCEDTWSGCIMGDTGYYLPKKFTQCNIEEYHDFLNSGGGACLFNKPSKLLDPPECGNGFIETGEECDCGTPAECVLEGAECCKKCTLTQDSQCSDGLCCKKCKFQPMGTVCREAVNDCDIRETCSGNSSQCAPNIHKMDGYSCDGVQGICFGGRCKTRDRQCKYIWGQKVTASDKYCYEKLNIEGTEKGNCGKDKDTWIQCNKRDVLCGYLLCTNIGNIPRLGELDGEITSTLVVQQGRTLNCSGGHVKLEEDVDLGYVEDGTPCGPQMMCLEHRCLPVASFNFSTCLSSKEGTICSGNGVCSNELKCVCNRHWIGSDCNTYFPHN 718
                                   242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712

Chain B from PDB  Type:PROTEIN  Length:486
 aligned with ADA22_HUMAN | Q9P0K1 from UniProtKB/Swiss-Prot  Length:906

    Alignment length:486
                                   242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712      
          ADA22_HUMAN   233 NVEEETKYIELMIVNDHLMFKKHRLSVVHTNTYAKSVVNMADLIYKDQLKTRIVLVAMETWATDNKFAISENPLITLREFMKYRRDFIKEKSDAVHLFSGSQFESSRSGAAYIGGICSLLKGGGVNEFGKTDLMAVTLAQSLAHNIGIISDKRKLASGECKCEDTWSGCIMGDTGYYLPKKFTQCNIEEYHDFLNSGGGACLFNKPSKLLDPPECGNGFIETGEECDCGTPAECVLEGAECCKKCTLTQDSQCSDGLCCKKCKFQPMGTVCREAVNDCDIRETCSGNSSQCAPNIHKMDGYSCDGVQGICFGGRCKTRDRQCKYIWGQKVTASDKYCYEKLNIEGTEKGNCGKDKDTWIQCNKRDVLCGYLLCTNIGNIPRLGELDGEITSTLVVQQGRTLNCSGGHVKLEEDVDLGYVEDGTPCGPQMMCLEHRCLPVASFNFSTCLSSKEGTICSGNGVCSNELKCVCNRHWIGSDCNTYFPHN 718
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3g5cB02 B:463-517 Echistatin                           --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeeehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeee...........hhhhhhhhhhhhhhhh......eeeeee.........eee...........eeeee..hhhhhhhhhhhhhhhhhh...hhhhhhhh........................hhhhhhhhhhhhhh..hhhhhh.........................hhhhhh......ee..ee......................eee.........ee..................ee....eeee..eeehhhhhhhhhhh......hhhhhhhhh...................hhhhh.................ee....eeeeeee..eeeeeee..ee.....ee.......eee..eee....eee.hhhh...........hhhh.eee.....eee...ee.....ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ------ADAM_MEPRO  PDB: B:239-438 UniProt: 239-438                                                                                                                                                             -----DISINTEGRIN_2  PDB: B:444-531 UniProt: 444-531                                          ------------------------------------------------------------------------------------------------------------------------------------------------------------------------EGF_1       ------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DISINTEGRIN_1       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3g5c B 233 NVEEETKYIELMIVNDHLMFKKHRLSVVHTNTYAKSVVNMADLIYKDQLKTRIVLVAMETWATDNKFAISENPLITLREFMKYRRDFIKEKSDAVHLFSGSQFESSRSGAAYIGGICSLLKGGGVNEFGKTDLMAVTLAQSLAHNIGIISDKRKLASGECKCEDTWSGCIMGDTGYYLPKKFTQCNIEEYHDFLNSGGGACLFNKPSKLLDPPECGNGFIETGEECDCGTPAECVLEGAECCKKCTLTQDSQCSDGLCCKKCKFQPMGTVCREAVNDCDIRETCSGNSSQCAPNIHKMDGYSCDGVQGICFGGRCKTRDRQCKYIWGQKVTASDKYCYEKLNIEGTEKGNCGKDKDTWIQCNKRDVLCGYLLCTNIGNIPRLGELDGEITSTLVVQQGRTLNCSGGHVKLEEDVDLGYVEDGTPCGPQMMCLEHRCLPVASFNFSTCLSSKEGTICSGNGVCSNELKCVCNRHWIGSDCNTYFPHN 718
                                   242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712

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 3G5C)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Few Secondary Structures (1120)

Architecture: Irregular (1120)

Topology: Echistatin (21)

Homologous Superfamily: Echistatin (21)

Human (Homo sapiens) (1)

1a	3g5cA02	A:463-517
1b	3g5cB02	B:463-517

(no "Pfam Domain" information available for 3G5C)

Asymmetric Unit(hide GO term definitions)

Chain A,B (ADA22_HUMAN | Q9P0K1)

molecular function
	GO:0005178	integrin binding	Interacting selectively and non-covalently with an integrin.
	GO:0004222	metalloendopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008237	metallopeptidase activity	Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0014037	Schwann cell differentiation	The process in which a relatively unspecialized cell acquires the specialized features of a Schwann cell. Schwann cells are found in the peripheral nervous system, where they insulate neurons and axons, and regulate the environment in which neurons function.
	GO:0008344	adult locomotory behavior	Locomotory behavior in a fully developed and mature organism.
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0007417	central nervous system development	The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
	GO:0042063	gliogenesis	The process that results in the generation of glial cells. This includes the production of glial progenitors and their differentiation into mature glia.
	GO:0022011	myelination in peripheral nervous system	The process in which neuronal axons and dendrites become coated with a segmented lipid-rich sheath (myelin) to enable faster and more energetically efficient conduction of electrical impulses. The sheath is formed by the cell membranes of Schwann cells in the peripheral nervous system. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier.
	GO:0007162	negative regulation of cell adhesion	Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric Unit
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	3g5c
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 12)

Sites (12, 12)

SS Bonds (40, 40)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (4, 8)

Exons (0, 0)

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