4AMT - JenaLib

Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE AT 2.6A OF HUMAN PRORENIN

Authors :   A. Zhou

Date :   13 Mar 12 (Deposition) - 20 Mar 13 (Release) - 20 Mar 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Hydrolase, Hormone, (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Zhou
The Crystal Structure Of Prorenin
To Be Published
PubMed: search

Molecule 1 - RENIN
	Chains	:	A
	EC Number	:	3.4.23.15
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293 EBNA
	Expression System Common	:	HUMAN
	Expression System Plasmid	:	PCEP4
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PRORENIN, ANGIOTENSINOGENASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 9)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	FUC	1	Ligand/Ion	ALPHA-L-FUCOSE
3	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 18)

No.	Name	Count	Type	Full Name
1	BMA	2	Ligand/Ion	BETA-D-MANNOSE
2	FUC	2	Ligand/Ion	ALPHA-L-FUCOSE
3	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	SO4	10	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:232 , LYS A:318	BINDING SITE FOR RESIDUE SO4 A1384
2	AC2	SOFTWARE	LYS A:116 , GLN A:137 , FUC A:1390	BINDING SITE FOR RESIDUE SO4 A1385
3	AC3	SOFTWARE	ILE A:176 , GLU A:177 , THR A:241 , ARG A:372	BINDING SITE FOR RESIDUE SO4 A1386
4	AC4	SOFTWARE	ASN A:57 , ASP A:60 , ALA A:272 , SER A:273 , TYR A:274	BINDING SITE FOR RESIDUE SO4 A1387
5	AC5	SOFTWARE	GLY A:70 , THR A:71 , ILE A:139 , THR A:141	BINDING SITE FOR RESIDUE SO4 A1388
6	AC6	SOFTWARE	ASN A:118 , THR A:120 , GLN A:137 , SO4 A:1385	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 118 RESIDUES 1389 TO 1392

Asymmetric Unit

No.	Residues
1	A:94	-	A:101
2	A:260	-	A:264
3	A:302	-	A:339

(no "Cis Peptide Bond" information available for 4AMT)

Asymmetric Unit (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_020375	R	33	W	RENI_HUMAN	Polymorphism	11571098	A	R	10	W
2	UniProt	VAR_035088	D	104	N	RENI_HUMAN	Disease (RTD)	868694193	A	D	81	N
3	UniProt	VAR_029171	Q	160	K	RENI_HUMAN	Polymorphism	11571083	A	Q	137	K
4	UniProt	VAR_020376	G	217	R	RENI_HUMAN	Polymorphism	11571117	A	G	194	R
5	UniProt	VAR_035087	R	230	K	RENI_HUMAN	Disease (RTD)	121917742	A	R	207	K

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

Biological Unit 1 (5, 10)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_020375	R	33	W	RENI_HUMAN	Polymorphism	11571098	A	R	10	W
2	UniProt	VAR_035088	D	104	N	RENI_HUMAN	Disease (RTD)	868694193	A	D	81	N
3	UniProt	VAR_029171	Q	160	K	RENI_HUMAN	Polymorphism	11571083	A	Q	137	K
4	UniProt	VAR_020376	G	217	R	RENI_HUMAN	Polymorphism	11571117	A	G	194	R
5	UniProt	VAR_035087	R	230	K	RENI_HUMAN	Disease (RTD)	121917742	A	R	207	K

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

Asymmetric Unit (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPTIDASE_A1	PS51767	Peptidase family A1 domain profile.	RENI_HUMAN	86-403	1	A:63-380
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	RENI_HUMAN	101-112 289-300	2	A:78-89 A:266-277

Biological Unit 1 (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPTIDASE_A1	PS51767	Peptidase family A1 domain profile.	RENI_HUMAN	86-403	2	A:63-380
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	RENI_HUMAN	101-112 289-300	4	A:78-89 A:266-277

Asymmetric Unit (10, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000272190	1b	ENSE00001952423	chr1:204135450-204135324	127	RENI_HUMAN	1-33	33	1	A:6-10	5
1.2	ENST00000272190	2	ENSE00000962217	chr1:204131291-204131141	151	RENI_HUMAN	33-83	51	1	A:10-60 (gaps)	51
1.3	ENST00000272190	3	ENSE00000962218	chr1:204130543-204130420	124	RENI_HUMAN	84-125	42	1	A:61-102	42
1.4	ENST00000272190	4	ENSE00001075102	chr1:204129806-204129688	119	RENI_HUMAN	125-164	40	1	A:102-141	40
1.5	ENST00000272190	5	ENSE00001075100	chr1:204128723-204128527	197	RENI_HUMAN	165-230	66	1	A:142-207	66
1.6	ENST00000272190	6	ENSE00001652153	chr1:204126497-204126489	9	RENI_HUMAN	230-233	4	1	A:207-208	2
1.7	ENST00000272190	7	ENSE00000962221	chr1:204125924-204125805	120	RENI_HUMAN	233-273	41	1	A:215-250	36
1.8	ENST00000272190	8	ENSE00001306111	chr1:204125447-204125306	142	RENI_HUMAN	273-320	48	1	A:250-297	48
1.9	ENST00000272190	9	ENSE00000962223	chr1:204125046-204124948	99	RENI_HUMAN	321-353	33	1	A:298-329	32
1.10a	ENST00000272190	10a	ENSE00001947658	chr1:204124305-204123947	359	RENI_HUMAN	354-406	53	1	A:336-383	48

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:349
 aligned with RENI_HUMAN | P00797 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:378
                                    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        
           RENI_HUMAN    29 TTFKRIFLKRMPSIRESLKERGVDMARLGPEWSQPMKRLTLGNTTSSVILTNYMDTQYYGEIGIGTPPQTFKVVFDTGSSNVWVPSSKCSRLYTACVYHKLFDASDSSSYKHNGTELTLRYSTGTVSGFLSQDIITVGGITVTQMFGEVTEMPALPFMLAEFDGVVGMGFIEQAIGRVTPIFDNIISQGVLKEDVFSFYYNRDSENSQSLGGQIVLGGSDPQHYEGNFHYINLIKTGVWQIQMKGVSVGSSTLLCEDGCLALVDTGASYISGSTSSIEKLMEALGAKKRLFDYVVKCNEGPTLPDISFHLGGKEYTLTSADYVFQESYSSKKLCTLAIHAMDIPPPTGPTWALGATFIRKFYTEFDRRNNRIGFALAR 406
               SCOP domains d4amta_ A: automated matches                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee.ee..hhhhhhhhhh.........-----------------.........eeeeeee.........................hhhhh........hhhhh...eeeeeeeeee....eeeeeeeeeeee................hhhhhh...........hhhhh.....hhhhhhhhh......eeeee....------...eeee...hhh.eeeeeeeee.......eeeeeeeee..eeee....eeeee......eeehhhhhhhhhhhhh........ee...hhhhh..eeeee..eeeeehhhhhh.------...ee..eee..........eeehhhhhhheeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----W----------------------------------------------------------------------N-------------------------------------------------------K--------------------------------------------------------R------------K-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------PEPTIDASE_A1  PDB: A:63-380 UniProt: 86-403                                                                                                                                                                                                                                                                                   --- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------ASP_PROTEASE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE---------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.1b --------------------------------------------------Exon 1.3  PDB: A:61-102 UniProt: 84-125   ---------------------------------------Exon 1.5  PDB: A:142-207 UniProt: 165-230                         --Exon 1.7  PDB: A:215-250 UniProt: 233-273-----------------------------------------------Exon 1.9  PDB: A:298-329         Exon 1.10a  PDB: A:336-383 UniProt: 354-406           Transcript 1 (1)
           Transcript 1 (2) ----Exon 1.2  PDB: A:10-60 (gaps) UniProt: 33-83       -----------------------------------------Exon 1.4  PDB: A:102-141                -----------------------------------------------------------------1.6 ---------------------------------------Exon 1.8  PDB: A:250-297 UniProt: 273-320       -------------------------------------------------------------------------------------- Transcript 1 (2)
                 4amt A   6 TTFKRIFLKRMPSIRESLKERGVDMARLGPE-----------------ILTNYMDTQYYGEIGIGTPPQTFKVVFDTGSSNVWVPSSKCSRLYTACVYHKLFDASDSSSYKHNGTELTLRYSTGTVSGFLSQDIITVGGITVTQMFGEVTEMPALPFMLAEFDGVVGMGFIEQAIGRVTPIFDNIISQGVLKEDVFSFYYNRD------LGGQIVLGGSDPQHYEGNFHYINLIKTGVWQIQMKGVSVGSSTLLCEDGCLALVDTGASYISGSTSSIEKLMEALGAKKRLFDYVVKCNEGPTLPDISFHLGGKEYTLTSADYVF------KKLCTLAIHAMDIPPPTGPTWALGATFIRKFYTEFDRRNNRIGFALAR 383
                                    15        25        35|        -        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205  |    215       225       235       245       255       265       275       285       295       305       315       325   |     -|      345       355       365       375        
                                                         36                54                                                                                                                                                       208    215                                                                                                               329    336

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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: Acid proteases (1120)

Superfamily: Acid proteases (1120)

Family: automated matches (23)

Protein domain: automated matches (23)

Human (Homo sapiens) [TaxId: 9606] (12)

d4amta_

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

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

Asymmetric Unit(hide GO term definitions)

Chain A (RENI_HUMAN | P00797)

molecular function
	GO:0004190	aspartic-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
	GO:0004175	endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0005159	insulin-like growth factor receptor binding	Interacting selectively and non-covalently with the insulin-like growth factor receptor.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
	GO:0050435	amyloid-beta metabolic process	The chemical reactions and pathways involving amyloid-beta, a glycoprotein associated with Alzheimer's disease, and its precursor, amyloid precursor protein (APP).
	GO:0002003	angiotensin maturation	The process leading to the attainment of the full functional capacity of angiotensin by conversion of renin substrate into mature angiotensin in the blood.
	GO:0048469	cell maturation	A developmental process, independent of morphogenetic (shape) change, that is required for a cell to attain its fully functional state.
	GO:0035690	cellular response to drug	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0042756	drinking behavior	The specific behavior of an organism relating to the intake of liquids, especially water.
	GO:0009755	hormone-mediated signaling pathway	A series of molecular signals mediated by the detection of a hormone.
	GO:0001822	kidney development	The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine.
	GO:0008584	male gonad development	The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure.
	GO:0001823	mesonephros development	The process whose specific outcome is the progression of the mesonephros over time, from its formation to the mature structure. In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the mesonephros will form the mature kidney.
	GO:0030163	protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0043408	regulation of MAPK cascade	Any process that modulates the frequency, rate or extent of signal transduction mediated by the MAP kinase (MAPK) cascade.
	GO:0008217	regulation of blood pressure	Any process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure.
	GO:0002016	regulation of blood volume by renin-angiotensin	The process in which the renin-angiotensin system controls the rate of fluid intake and output into the blood.
	GO:0002018	renin-angiotensin regulation of aldosterone production	The process in which an increase in active angiotensin stimulates the adrenal cortices to secrete aldosterone.
	GO:0051591	response to cAMP	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 cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
	GO:0070305	response to cGMP	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 cGMP (cyclic GMP, guanosine 3',5'-cyclophosphate) stimulus.
	GO:0042493	response to drug	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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0035902	response to immobilization stress	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 being rendered immobile.
	GO:0032496	response to lipopolysaccharide	Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0010033	response to organic substance	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 an organic substance stimulus.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0005764	lysosome	A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
	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.

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	4amt
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1bbs	RENIN
1bil
1bim
1hrn	RENIN COMPLEXED WITH POLYHYDROXYMONOAMIDE INHIBITOR BILA 980
1rne	RENIN (ACTIVATED, GLYCOSYLATED, INHIBITED) COMPLEX WITH CGP 38'560
2bks	CRYSTAL STRUCTURE OF RENIN-PF00074777 COMPLEX
2bkt	CRYSTAL STRUCTURE OF RENIN-PF00257567 COMPLEX
2fs4	KETOPIPERAZINE-BASED RENIN INHIBITORS: OPTIMIZATION OF THEC RING
2g1n	KETOPIPERAZINE-BASED RENIN INHIBITORS: OPTIMIZATION OF THE "C" RING
2g1o	KETOPIPERAZINE-BASED RENIN INHIBITORS: OPTIMIZATION OF THE "C" RING
2g1r	KETOPIPERAZINE-BASED RENIN INHIBITORS: OPTIMIZATION OF THEC RING
2g1s	KETOPIPERAZINE-BASED RENIN INHIBITORS: OPTIMIZATION OF THEC RING
2g1y	KETOPIPERAZINE-BASED RENIN INHIBITORS: OPTIMIZATION OF THE "C" RING
2g20	KETOPIPERAZINE-BASED RENIN INHIBITORS: OPTIMIZATION OF THEC RING
2g21	KETOPIPERAZINE-BASED RENIN INHIBITORS: OPTIMIZATION OF THE "C" RING
2g22	KETOPIPERAZINE-BASED RENIN INHIBITORS: OPTIMIZATION OF THE "C" RING
2g24	KETOPIPERAZINE-BASED RENIN INHIBITORS: OPTIMIZATION OF THE "C" RING
2g26	KETOPIPERAZINE-BASED RENIN INHIBITORS: OPTIMIZATION OF THE "C" RING
2g27	KETOPIPERAZINE-BASED RENIN INHIBITORS: OPTIMIZATION OF THE "C" RING
2ren	RENIN
2v0z	CRYSTAL STRUCTURE OF RENIN WITH INHIBITOR 10 (ALISKIREN)
2v10	CRYSTAL STRUCTURE OF RENIN WITH INHIBITOR 9
2v11	CRYSTAL STRUCTURE OF RENIN WITH INHIBITOR 6
2v12	CRYSTAL STRUCTURE OF RENIN WITH INHIBITOR 8
2v13	CRYSTAL STRUCTURE OF RENIN WITH INHIBITOR 7
2v16	CRYSTAL STRUCTURE OF RENIN WITH INHIBITOR 3
2x0b	CRYSTAL STRUCTURE OF HUMAN ANGIOTENSINOGEN COMPLEXED WITH RENIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (6, 6)

SS Bonds (3, 3)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (5, 5)

PROSITE Motifs (2, 3)

Exons (10, 10)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (34, 34)

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Related Entries Specified in the PDB File