9PAP - JenaLib

Title :   STRUCTURE OF PAPAIN REFINED AT 1.65 ANGSTROMS RESOLUTION

Authors :   I. G. Kamphuis, J. Drenth

Date :   31 Mar 86 (Deposition) - 24 Oct 86 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

Chains :   Asym./Biol. Unit : A

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

Reference :   I. G. Kamphuis, K. H. Kalk, M. B. Swarte, J. Drenth
Structure Of Papain Refined At 1. 65 A Resolution
J. Mol. Biol. V. 179 233 1984
PubMed-ID: 6502713 | Reference-DOI: 10.1016/0022-2836(84)90467-4
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 30)

Sites (29, 29)

Asymmetric Unit (29, 29)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR A:78 , LYS A:106 , HOH A:341 , HOH A:432	BINDING SITE FOR RESIDUE MOH A 214
02	AC2	SOFTWARE	LEU A:143 , ARG A:145 , GLY A:146	BINDING SITE FOR RESIDUE MOH A 215
03	AC3	SOFTWARE	ILE A:40 , ARG A:41	BINDING SITE FOR RESIDUE MOH A 216
04	AC4	SOFTWARE	ALA A:126 , ASN A:127	BINDING SITE FOR RESIDUE MOH A 217
05	AC5	SOFTWARE	SER A:97 , GLY A:101 , TYR A:103	BINDING SITE FOR RESIDUE MOH A 218
06	AC6	SOFTWARE	CYS A:153 , GLY A:154 , CYS A:200 , HOH A:299 , HOH A:413	BINDING SITE FOR RESIDUE MOH A 219
07	AC7	SOFTWARE	SER A:124 , ASN A:127 , GLN A:128	BINDING SITE FOR RESIDUE MOH A 220
08	AC8	SOFTWARE	OCS A:25 , GLY A:65 , GLY A:66	BINDING SITE FOR RESIDUE MOH A 221
09	AC9	SOFTWARE	HOH A:383	BINDING SITE FOR RESIDUE MOH A 222
10	ACT	UNKNOWN	HIS A:159 , ASN A:175	NULL
11	BC1	SOFTWARE	ARG A:145 , GLY A:194	BINDING SITE FOR RESIDUE MOH A 223
12	BC2	SOFTWARE	ARG A:111 , GLN A:112 , HOH A:336	BINDING SITE FOR RESIDUE MOH A 224
13	BC3	SOFTWARE	PRO A:68 , HOH A:282	BINDING SITE FOR RESIDUE MOH A 225
14	BC4	SOFTWARE	HOH A:363	BINDING SITE FOR RESIDUE MOH A 227
15	BC5	SOFTWARE	ASP A:140 , GLY A:151 , PRO A:152 , HOH A:390	BINDING SITE FOR RESIDUE MOH A 228
16	BC6	SOFTWARE	PRO A:15 , HOH A:379	BINDING SITE FOR RESIDUE MOH A 229
17	BC7	SOFTWARE	GLY A:20 , SER A:21 , HOH A:414	BINDING SITE FOR RESIDUE MOH A 230
18	BC8	SOFTWARE	TYR A:78	BINDING SITE FOR RESIDUE MOH A 231
19	BC9	SOFTWARE	ASN A:18 , GLY A:20	BINDING SITE FOR RESIDUE MOH A 232
20	CC1	SOFTWARE	ARG A:188 , MOH A:235 , HOH A:404	BINDING SITE FOR RESIDUE MOH A 233
21	CC2	SOFTWARE	ASN A:64	BINDING SITE FOR RESIDUE MOH A 234
22	CC3	SOFTWARE	GLY A:147 , GLU A:183 , ARG A:188 , MOH A:233	BINDING SITE FOR RESIDUE MOH A 235
23	CC4	SOFTWARE	TYR A:208	BINDING SITE FOR RESIDUE MOH A 236
24	CC5	SOFTWARE	THR A:42 , ASN A:44 , ASN A:46 , TYR A:82 , HOH A:287 , HOH A:328	BINDING SITE FOR RESIDUE MOH A 237
25	CC6	SOFTWARE	TYR A:82 , HOH A:416	BINDING SITE FOR RESIDUE MOH A 238
26	CC7	SOFTWARE	ILE A:37 , ARG A:41 , ASN A:127 , GLN A:128 , HOH A:388	BINDING SITE FOR RESIDUE MOH A 239
27	CC8	SOFTWARE	TYR A:116 , SER A:196	BINDING SITE FOR RESIDUE MOH A 240
28	CC9	SOFTWARE	GLN A:142 , HOH A:381	BINDING SITE FOR RESIDUE MOH A 241
29	DC1	SOFTWARE	ARG A:59 , TYR A:61 , TYR A:67	BINDING SITE FOR RESIDUE MOH A 242

SS Bonds (3, 3)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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

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Chain A from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains d9papa_ A: Papain                                                                                                                                                                                                    SCOP domains
               CATH domains 9papA00 A:1-212 Cysteine proteinases                                                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee................hhhhhhhhhhhhhhhhhhhh......hhhhhhhh.........hhhhhhhhhhhh.............................eeeeee...hhhhhhhhhhhh.eeeee...hhhhhh..............eeeeeeeeee..eeeeee.........eeeeeee..............eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 9pap A   1 IPEYVDWRQKGAVTPVKNQGSCGScWAFSAVVTIEGIIKIRTGNLNQYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNQGALLYSIANQPVSVVLQAAGKDFQLYRGGIFVGPCGNKVDHAVAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN 212
                                    10        20    |   30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  
                                                   25-OCS

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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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

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the following images were kindly provided by the protease and protease inhibitor web server prolysis.
	*The structure of papain (PDB code: 9pap), the archetype of cysteine proteases of the papain family, isolated from the latex of the plant Carica papaya* (mono** [ mono JPEG format ]).
	A comparison of papain (PDB code: 9pap) and human cathepsin B (PDB code: 1huc). The occluding loop of human cathepsin B reduces the access of protease inhibitors to the active site. For instance, the affinity constant (Ki) of chicken cystatin for human cathepsin B is reduced by a factor 340 as compared to papain (mono). [ mono JPEG format ]
	A structural superimposition of papain (PDB code: 9pap) and human cathepsin B (PDB code: 1huc) (mono). [ mono JPEG format ]

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