2RMP - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   RMP-PEPSTATIN A COMPLEX

Authors :   J. Yang, J. W. Quail

Date :   30 May 97 (Deposition) - 17 Sep 97 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym./Biol. Unit : A,B

Keywords :   Aspartic Proteinase, Pepstatin A, Aspartyl Protease-Peptide Complex, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Yang, J. W. Quail
Structure Of The Rhizomucor Miehei Aspartic Proteinase Complexed With The Inhibitor Pepstatin A At 2. 7 A Resolution.
Acta Crystallogr. , Sect. D V. 55 625 1999
PubMed-ID: 10089458 | Reference-DOI: 10.1107/S0907444998013961

Molecule 1 - MUCOROPEPSIN
	Chains	:	A
	EC Number	:	3.4.23.23
	Organism Common	:	MUCOR MIEHEI
	Organism Scientific	:	RHIZOMUCOR MIEHEI
	Organism Taxid	:	4839
	Synonym	:	MUCOR RENIN, RHIOMUCOR MIEHEI ASPARTIC PROTEINASE

Molecule 2 - PEPSTATIN
	Chains	:	B
	Organism Scientific	:	STREPTOMYCES
	Organism Taxid	:	1883
	Other Details	:	INHIBITOR PEPSTATIN A IS BOUND TO THE ENZYME
	Other Details - Source	:	STREPTOMYCES (PEPSTATIN A WAS ISOLATED FROM STREPTOMYCES)

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 6)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	IVA	1	Mod. Amino Acid	ISOVALERIC ACID
3	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	STA	2	Mod. Amino Acid	STATINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:5 , SER A:6 , VAL A:7 , ASP A:8 , THR A:9 , PRO A:10 , GLY A:11 , TYR A:12 , TYR A:13 , ASP A:14 , PHE A:15 , LEU A:17 , GLU A:18 , GLU A:19 , TYR A:20 , ALA A:21 , ILE A:22 , VAL A:24 , SER A:25 , ILE A:26 , GLY A:27 , PRO A:29 , GLY A:30 , LEU A:34 , LEU A:35 , LEU A:36 , PHE A:37 , ASP A:38 , THR A:39 , GLY A:40 , SER A:41 , SER A:42 , ASP A:43 , THR A:44 , TRP A:45 , VAL A:46 , PRO A:47 , HIS A:48 , CYS A:51 , GLU A:55 , GLY A:56 , VAL A:58 , GLY A:59 , ARG A:61 , PHE A:63 , SER A:66 , SER A:68 , SER A:69 , THR A:70 , PHE A:71 , LYS A:72 , THR A:74 , TYR A:76 , ASN A:77 , LEU A:78 , IVA B:700 , VAL B:701 , VAL B:702 , STA B:703 , ALA B:704 , STA B:705	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 79 RESIDUES 79 TO 602
2	AC2	SOFTWARE	GLU A:19 , LEU A:36 , ASP A:38 , GLY A:40 , TYR A:82 , GLY A:83 , THR A:84 , PRO A:117 , LEU A:132 , PHE A:210 , ASP A:237 , GLY A:239 , THR A:240 , ASN A:241 , LEU A:321 , ILE A:329	BINDING SITE FOR CHAIN B OF PEPSTATIN

Asymmetric/Biological Unit

No.	Residues
1	A:51	-	A:57
2	A:272	-	A:316

Asymmetric/Biological Unit

No.	Residues
1	Thr A:28	-	Pro A:29

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CARP_RHIMI_001 *	G	262	S	CARP_RHIMI	---	---	A	G	193	S
	* ID not provided by source

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

Asymmetric/Biological Unit (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPTIDASE_A1	PS51767	Peptidase family A1 domain profile.	CARP_RHIMI	89-421	1	A:20-352
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	CARP_RHIMI	104-115 303-314	2	A:35-46 A:234-245

(no "Exon" information available for 2RMP)

Asymmetric/Biological 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:358
 aligned with CARP_RHIMI | P00799 from UniProtKB/Swiss-Prot  Length:430

    Alignment length:358
                                    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        
           CARP_RHIMI    73 DGSVDTPGYYDFDLEEYAIPVSIGTPGQDFLLLFDTGSSDTWVPHKGCTKSEGCVGSRFFDPSASSTFKATNYNLNITYGTGGANGLYFEDSIAIGDITVTKQILAYVDNVRGPTAEQSPNADIFLDGLFGAAYPDNTAMEAEYGSTYNTVHVNLYKQGLISSPLFSVYMNTNSGTGEVVFGGVNNTLLGGDIAYTDVMSRYGGYYFWDAPVTGITVDGSAAVRFSRPQAFTIDTGTNFFIMPSSAASKIVKAALPDATETQQGWVVPCASYQNSKSTISIVMQKSGSSSDTIEISVPVSKMLLPVDQSNETCMFIILPDGGNQYIVGNLFLRFFVNVYDFGNNRIGFAPLASAYENE 430
               SCOP domains d2rmpa_ A: Acid protease                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains --2rmpA01 A:6-186 Acid Proteases                                                                                                                                                       2rmpA02 A:187-359 Acid Proteases                                                                                                                                             -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee...eeeeeeeee....eeeeeeee....eeeee.....hhhh........hhh....ee...eeeee....eeeeeeee.eeee..eeeeeeeeeeeeeee.hhhh..........eeee...hhhhhhhhhh......hhhhhhh........eeeeee...eeeeeee....hhh.....eeee...........eeeeeeeee...eeee....eeee.......eee.hhhhhhhhhhh....eee..eeeee..hhh....eeeeeee......eeeeeeeehhhh.eee.....eeee.eee......ee.hhhh..eeeeee....eeeeee..hhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----------------PEPTIDASE_A1  PDB: A:20-352 UniProt: 89-421                                                                                                                                                                                                                                                                                                  --------- PROSITE (1)
                PROSITE (2) -------------------------------ASP_PROTEASE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE-------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rmp A   4 DGSVDTPGYYDFDLEEYAIPVSIGTPGQDFLLLFDTGSSDTWVPHKGCTKSEGCVGSRFFDPSASSTFKATNYNLNITYGTGGANGLYFEDSIAIGDITVTKQILAYVDNVRGPTAEQSPNADIFLDGLFGAAYPDNTAMEAEYGSTYNTVHVNLYKQGLISSPLFSVYMNTNSGTGEVVFGGVNNTLLGGDIAYTDVMSRYGGYYFWDAPVTGITVDGSAAVRFSRPQAFTIDTGTNFFIMPSSAASKIVKAALPDATETQQGWVVPCASYQNSKSTISIVMQKSGSSSDTIEISVPVSKMLLPVDQSNETCMFIILPDGGNQYIVGNLFLRFFVNVYDFGNNRIGFAPLASAYENE 361
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353

Chain B from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 2rmp B 700 xVVxAx 705
                            |  | |
                          700-IVA|
                             703-STA
                               705-STA

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/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: Acid proteases (1120)

Superfamily: Acid proteases (1120)

Family: Pepsin-like (505)

Protein domain: Acid protease (44)

Rhizomucor miehei [TaxId: 4839] (2)

d2rmpa_

Asymmetric/Biological Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Cathepsin D, subunit A; domain 1 (745)

Homologous Superfamily: Acid Proteases (745)

Mucor miehei (Rhizomucor miehei) (2)

1a	2rmpA02	A:187-359
1b	2rmpA01	A:6-186

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CARP_RHIMI | P00799)

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: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: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.
biological process
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Asymmetric/Biological Unit
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		Thr A:28 - Pro A:29	[ RasMol ]

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

Description

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Ligands, Modified Residues, Ions (4, 6)

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SS Bonds (2, 2)

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