4K1R - JenaLib

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Title :   CRYSTAL STRUCTURE OF SCHIZOSACCHAROMYCES POMBE SST2 CATALYTIC DOMAIN AND UBIQUITIN

Authors :   R. K. Shrestha, C. Das

Date :   05 Apr 13 (Deposition) - 23 Apr 14 (Release) - 18 Jun 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.63

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

Keywords :   Helix-Beta-Helix Sandwich, Ubiquitin, Deubiquitination, Zinc Metalloprotease, Cytosol, Endosome, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. K. Shrestha, J. A. Ronau, C. W. Davies, R. G. Guenette, E. R. Strieter L. N. Paul, C. Das
Insights Into The Mechanism Of Deubiquitination By Jamm Deubiquitinases From Cocrystal Structures Of The Enzyme Wit The Substrate And Product.
Biochemistry V. 53 3199 2014
PubMed-ID: 24787148 | Reference-DOI: 10.1021/BI5003162

Molecule 1 - AMSH-LIKE PROTEASE SST2
	Chains	:	A, C
	EC Number	:	3.4.19.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6-P1
	Expression System Strain	:	ROSETTA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN (UNP RESIDUES 246-436)
	Gene	:	SPAC19B12.10, SST2
	Organism Common	:	FISSION YEAST
	Organism Scientific	:	SCHIZOSACCHAROMYCES POMBE
	Organism Taxid	:	284812
	Strain	:	972 / ATCC 24843
	Synonym	:	SUPPRESSOR OF STE12 DELETION PROTEIN 2

Molecule 2 - POLYUBIQUITIN-C
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6-P1
	Expression System Strain	:	ROSETTA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	UBC
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	UBIQUITIN

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 18)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	EDO	10	Ligand/Ion	1,2-ETHANEDIOL
3	ZN	6	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 10)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	10	Ligand/Ion	1,2-ETHANEDIOL
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:304 , HIS A:332 , CL A:504 , GLU C:327	BINDING SITE FOR RESIDUE ZN A 501
02	AC2	SOFTWARE	HIS A:341 , HIS A:343 , ASP A:354 , GLY B:76	BINDING SITE FOR RESIDUE ZN A 502
03	AC3	SOFTWARE	HIS A:356 , CYS A:397 , HIS A:404 , HIS A:406	BINDING SITE FOR RESIDUE ZN A 503
04	AC4	SOFTWARE	HIS A:304 , HIS A:332 , GLN A:428 , ZN A:501 , GLU C:327 , PHE C:328	BINDING SITE FOR RESIDUE CL A 504
05	AC5	SOFTWARE	GLN A:329 , ASN A:333 , LEU A:334 , LEU A:335 , LEU B:8	BINDING SITE FOR RESIDUE EDO A 505
06	AC6	SOFTWARE	GLN A:346 , PHE A:349 , HOH A:700 , HOH A:701 , HOH A:710 , GLY B:76	BINDING SITE FOR RESIDUE EDO A 506
07	AC7	SOFTWARE	THR A:345 , SER A:376 , LYS A:377	BINDING SITE FOR RESIDUE EDO A 507
08	AC8	SOFTWARE	LYS A:270 , SER A:380 , GLY A:381 , ILE A:382 , GLN A:416 , GLU A:422	BINDING SITE FOR RESIDUE EDO A 508
09	AC9	SOFTWARE	LYS A:294 , ARG A:296	BINDING SITE FOR RESIDUE EDO A 509
10	BC1	SOFTWARE	HOH A:633 , THR B:7 , LEU B:8 , LEU B:69 , VAL B:70 , LEU B:71	BINDING SITE FOR RESIDUE EDO B 101
11	BC2	SOFTWARE	HIS C:341 , HIS C:343 , ASP C:354 , GLY D:76	BINDING SITE FOR RESIDUE ZN C 501
12	BC3	SOFTWARE	HIS C:356 , CYS C:397 , HIS C:404 , HIS C:406	BINDING SITE FOR RESIDUE ZN C 502
13	BC4	SOFTWARE	GLU A:327 , HIS C:304 , HIS C:332 , CL C:504	BINDING SITE FOR RESIDUE ZN C 503
14	BC5	SOFTWARE	GLU A:327 , PHE A:328 , HIS C:304 , HIS C:332 , GLN C:428 , ZN C:503	BINDING SITE FOR RESIDUE CL C 504
15	BC6	SOFTWARE	GLU A:311 , THR A:316 , CYS A:317 , GLY A:318 , HOH A:649 , ARG B:74 , HOH B:205 , THR C:313 , ASP C:315	BINDING SITE FOR RESIDUE EDO C 505
16	BC7	SOFTWARE	ASN C:333 , LEU C:334 , HOH C:682 , HOH C:683 , LEU D:8 , HOH D:219	BINDING SITE FOR RESIDUE EDO C 506
17	BC8	SOFTWARE	SER C:352 , VAL C:353 , HIS C:356 , GLY C:401 , LEU C:402 , HIS C:404 , HOH C:658	BINDING SITE FOR RESIDUE EDO C 507
18	BC9	SOFTWARE	HOH C:631 , THR D:7 , LEU D:8 , LEU D:69 , VAL D:70 , LEU D:71	BINDING SITE FOR RESIDUE EDO D 101

(no "SS Bond" information available for 4K1R)

Asymmetric Unit

No.	Residues
1	Asp A:387	-	Pro A:388
2	Gln A:416	-	Pro A:417
3	Asp C:387	-	Pro C:388
4	Gln C:416	-	Pro C:417

(no "SAP(SNP)/Variant" information available for 4K1R)

(no "PROSITE Motif" information available for 4K1R)

(no "Exon" information available for 4K1R)

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:189
                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.....ee..eeee.hhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeeee..eee....eee.hhhhhhhhhhhhh.eeeeeeee........hhhhhhhhhhhhhhh...eeeeeehhhheeeeeee..hhhhhhhhhh.............eee......eeee....eeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k1r A 247 TFKIHAYTEGGKPLRTIYLPKLLKKVFLDVVKPNTKKNLETCGILCGKLRQNAFFITHLVIPLQEATSDTCGTTDEASLFEFQDKHNLLTLGWIHTHPTQTCFMSSVDLHTHCSYQLMLPEAIAIVMAPSKNTSGIFRLLDPEGLQTIVKCRKPGLFHPHEGKVYTMVAQPGHVREINSKLQVVDLRVK 435
                                   256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426

Chain B from PDB  Type:PROTEIN  Length:77
                                                                                                             
               SCOP domains ----------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeee....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee..ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 4k1r B   0 SMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  76
                                     9        19        29        39        49        59        69

Chain C from PDB  Type:PROTEIN  Length:189
                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.....ee..eeee.hhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeeee..eee....eee.hhhhhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhhh...eeeeeehhhheeeeeee..hhhhhhhhhh.............eee......eeee....eeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k1r C 247 TFKIHAYTEGGKPLRTIYLPKLLKKVFLDVVKPNTKKNLETCGILCGKLRQNAFFITHLVIPLQEATSDTCGTTDEASLFEFQDKHNLLTLGWIHTHPTQTCFMSSVDLHTHCSYQLMLPEAIAIVMAPSKNTSGIFRLLDPEGLQTIVKCRKPGLFHPHEGKVYTMVAQPGHVREINSKLQVVDLRVK 435
                                   256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426

Chain D from PDB  Type:PROTEIN  Length:76
                                                                                                            
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee..ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 4k1r D   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  76
                                    10        20        30        40        50        60        70

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 4K1R)

(no "CATH Domain" information available for 4K1R)

(no "Pfam Domain" information available for 4K1R)

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	Cis Peptide Bonds
		Asp A:387 - Pro A:388	[ RasMol ]
		Asp C:387 - Pro C:388	[ RasMol ]
		Gln A:416 - Pro A:417	[ RasMol ]
		Gln C:416 - Pro C:417	[ RasMol ]

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2znv	AMSH-LP E292A BOUND TO LYS63- LINKED UBIQUITIN DIMER

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 18)

Sites (18, 18)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

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Exons (0, 0)

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Gene Ontology (94, 95)

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