Het-PDB Navi2 (PDB: 4GK7)

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Ligands
Code	Name		Style	Show	Link

Non-standard Residues
Code	Name	Show
0JT	(4r)-4-amino-5-methylhexanoic acid
LYH	3,4 ene-lysine

Glycosylation
Code	Name	Emphasize

Modification
Code	Name	Show
MH9	(2e,4e)-dodeca-2,4-dienoic acid

Download interaction data: 4GK7

Code :

4GK7 PDBj RCSB PDB PDBe

Header :

hydrolase/hydrolase inhibitor

Title :

yeast 20S proteasome in complex with the Syringolin-Glidobactin chimera

Release Data :

2012-08-29

Compound :

mol_id	molecule	chains	synonym
1	Proteasome component Y7	A,O	Macropain subunit Y7, Multicatalytic endopeptidase complex subunit Y7, Proteinase YSCE subunit 7
	ec: 3.4.25.1

mol_id	molecule	chains	synonym
2	Proteasome component Y13	B,P	Macropain subunit Y13, Multicatalytic endopeptidase complex subunit Y13, Proteinase YSCE subunit 13
	ec: 3.4.25.1

mol_id	molecule	chains	synonym
3	Proteasome component PRE6	C,Q	Macropain subunit PRE6, Multicatalytic endopeptidase complex subunit PRE6, Proteinase YSCE subunit PRE6
	ec: 3.4.25.1

mol_id	molecule	chains	synonym
4	Proteasome component PUP2	D,R	Macropain subunit PUP2, Multicatalytic endopeptidase complex subunit PUP2, Proteinase YSCE subunit PUP2
	ec: 3.4.25.1

mol_id	molecule	chains	synonym
5	Proteasome component PRE5	E,S	Macropain subunit PRE5, Multicatalytic endopeptidase complex subunit PRE5, Proteinase YSCE subunit PRE5
	ec: 3.4.25.1

mol_id	molecule	chains	synonym
6	Proteasome component C1	F,T	Macropain subunit C1, Multicatalytic endopeptidase complex subunit C1, Proteinase YSCE subunit 1
	ec: 3.4.25.1

mol_id	molecule	chains	synonym
7	Proteasome component C7-alpha	G,U	Macropain subunit C7-alpha, Multicatalytic endopeptidase complex C7, Proteasome component Y8, Proteinase YSCE subunit 7, SCL1 suppressor protein
	ec: 3.4.25.1

mol_id	molecule	chains	synonym
8	Proteasome component PUP1	H,V	Macropain subunit PUP1, Multicatalytic endopeptidase complex subunit PUP1, Proteinase YSCE subunit PUP1
	ec: 3.4.25.1

mol_id	molecule	chains	synonym
9	Proteasome component PUP3	I,W	Macropain subunit PUP3, Multicatalytic endopeptidase complex subunit PUP3
	ec: 3.4.25.1

mol_id	molecule	chains	synonym
10	Proteasome component C11	J,X	Macropain subunit C11, Multicatalytic endopeptidase complex subunit C11, Proteinase YSCE subunit 11
	ec: 3.4.25.1

mol_id	molecule	chains	synonym
11	Proteasome component PRE2	K,Y	Macropain subunit PRE2, Multicatalytic endopeptidase complex subunit PRE2, Proteinase YSCE subunit PRE2
	ec: 3.4.25.1

mol_id	molecule	chains	synonym
12	Proteasome component C5	L,Z	Multicatalytic endopeptidase complex subunit C5
	ec: 3.4.25.1

mol_id	molecule	chains	synonym
13	Proteasome component PRE4	M,a	Macropain subunit PRE4, Multicatalytic endopeptidase complex subunit PRE4, Proteinase YSCE subunit PRE4
	ec: 3.4.25.1

mol_id	molecule	chains	synonym
14	Proteasome component PRE3	N,b	Macropain subunit PRE3, Multicatalytic endopeptidase complex subunit PRE3, Proteinase YSCE subunit PRE3
	ec: 3.4.25.1

mol_id	molecule	chains	synonym
15	SYRINGOLIN-GLIDOBACTIN CHIMERA	1,2,3,4,5,6	BOUND FORM OF CYCLIC SYLA-GLBA HYBRID

Source :

mol_id	organism_scientific	organism_common
1	Saccharomyces cerevisiae (taxid:559292)	Baker's yeast
	strain: ATCC 204508 / S288c

mol_id	organism_scientific	organism_common
2	Saccharomyces cerevisiae (taxid:559292)	Baker's yeast
	strain: ATCC 204508 / S288c

mol_id	organism_scientific	organism_common
3	Saccharomyces cerevisiae (taxid:559292)	Baker's yeast
	strain: ATCC 204508 / S288c

mol_id	organism_scientific	organism_common
4	Saccharomyces cerevisiae (taxid:559292)	Baker's yeast
	strain: ATCC 204508 / S288c

mol_id	organism_scientific	organism_common
5	Saccharomyces cerevisiae (taxid:559292)	Baker's yeast
	strain: ATCC 204508 / S288c

mol_id	organism_scientific	organism_common
6	Saccharomyces cerevisiae (taxid:559292)	Baker's yeast
	strain: ATCC 204508 / S288c

mol_id	organism_scientific	organism_common
7	Saccharomyces cerevisiae (taxid:559292)	Baker's yeast
	strain: ATCC 204508 / S288c

mol_id	organism_scientific	organism_common
8	Saccharomyces cerevisiae (taxid:559292)	Baker's yeast
	strain: ATCC 204508 / S288c

mol_id	organism_scientific	organism_common
9	Saccharomyces cerevisiae (taxid:559292)	Baker's yeast
	strain: ATCC 204508 / S288c

mol_id	organism_scientific	organism_common
10	Saccharomyces cerevisiae (taxid:559292)	Baker's yeast
	strain: ATCC 204508 / S288c

mol_id	organism_scientific	organism_common
11	Saccharomyces cerevisiae (taxid:559292)	Baker's yeast
	strain: ATCC 204508 / S288c

mol_id	organism_scientific	organism_common
12	Saccharomyces cerevisiae (taxid:559292)	Baker's yeast
	strain: ATCC 204508 / S288c

mol_id	organism_scientific	organism_common
13	Saccharomyces cerevisiae (taxid:559292)	Baker's yeast
	strain: ATCC 204508 / S288c

mol_id	organism_scientific	organism_common
14	Saccharomyces cerevisiae (taxid:559292)	Baker's yeast
	strain: ATCC 204508 / S288c

mol_id	organism_scientific	organism_common
15	Synthetic construct (taxid:32630)	Synthetic
	synthetic: yes

Authors :

Groll, M., Stein, M.L., Bachmann, A.

Keywords :

proteasome, cancer, protein degradation, inhibition, natural product derivative, NTN-hydrolase, hydrolase-hydrolase inhibitor complex, 12-membered dipeptide-macrolactam

Exp. method :

X-RAY DIFFRACTION ( 2.80 Å )

Citation :

Activity enhancement of the synthetic syrbactin proteasome inhibitor hybrid and biological evaluation in tumor cells.

Archer, C.R.,Groll, M.,Stein, M.L. et al.
(2012) Biochemistry 51 : 6880 - 6888

PubMed: 22870914
DOI: 10.1021/bi300841r

Chain :	A, O
UniProt :	P23639 (PSA2_YEAST)
Reaction :	-

Chain :	B, P
UniProt :	P23638 (PSA3_YEAST)
Reaction :	-

Chain :	C, Q
UniProt :	P40303 (PSA4_YEAST)
Reaction :	-

Chain :	D, R
UniProt :	P32379 (PSA5_YEAST)
Reaction :	-

Chain :	E, S
UniProt :	P40302 (PSA6_YEAST)
Reaction :	-

Chain :	F, T
UniProt :	P21242 (PSA7_YEAST)
Reaction :	-

Chain :	G, U
UniProt :	P21243 (PSA1_YEAST)
Reaction :	-

Chain :

H, V

UniProt :

P25043 (PSB2_YEAST)

Reaction:	EC:	Evidence:
Reaction:	Physiological Direction:	Evidence:
Cleavage of peptide bonds with very broad specificity.	3.4.25.1	-
Cleavage of peptide bonds with very broad specificity.	-	-

Chain :	I, W
UniProt :	P25451 (PSB3_YEAST)
Reaction :	-

Chain :	J, X
UniProt :	P22141 (PSB4_YEAST)
Reaction :	-

Chain :

K, Y

UniProt :

P30656 (PSB5_YEAST)

Reaction:	EC:	Evidence:
Reaction:	Physiological Direction:	Evidence:
Cleavage of peptide bonds with very broad specificity.	3.4.25.1	-
Cleavage of peptide bonds with very broad specificity.	-	-

Chain :	L, Z
UniProt :	P23724 (PSB6_YEAST)
Reaction :	-

Chain :	M, a
UniProt :	P30657 (PSB7_YEAST)
Reaction :	-

Chain :

N, b

UniProt :

P38624 (PSB1_YEAST)

Reaction:	EC:	Evidence:
Reaction:	Physiological Direction:	Evidence:
Cleavage of peptide bonds with very broad specificity.	3.4.25.1	-
Cleavage of peptide bonds with very broad specificity.	-	-

PDB ID: 4GK7

Hetero Atom Contents

Structure summary

Reaction