Het-PDB Navi2 (PDB: 4JT0)

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Ligands
Code	Name		Style	Show	Link
0L1	Hexanedioic acid				PoSSuM
MES	2-(N-morpholino)-ethanesulfonic acid				PoSSuM

Non-standard Residues
Code	Name	Show
ACA	6-aminohexanoic acid
RE0	3-[(3r)-3-hydroxy-2-oxo-2,3-dihydro-1h-indol-3-yl]-L-alanine
TY5	O-benzyl-L-tyrosine

Glycosylation
Code	Name	Emphasize

Modification
Code	Name	Show
ABN	Benzylamine

Download interaction data: 4JT0

Code :

4JT0 PDBj RCSB PDB PDBe

Header :

HYDROLASE/HYDROLASE INHIBITOR

Title :

Yeast 20S proteasome in complex with the dimerized linear mimetic of TMC-95A - yCP:4a

Release Data :

2013-05-01

Compound :

mol_id	molecule	chains	synonym
1	Proteasome subunit alpha type-2	A,O	Macropain subunit Y7, Multicatalytic endopeptidase complex subunit Y7, Proteasome component Y7, Proteinase YSCE subunit 7
	ec: 3.4.25.1

mol_id	molecule	chains	synonym
2	Proteasome subunit alpha type-3	B,P	Macropain subunit Y13, Multicatalytic endopeptidase complex subunit Y13, Proteasome component Y13, Proteinase YSCE subunit 13
	ec: 3.4.25.1

mol_id	molecule	chains	synonym
3	Proteasome subunit alpha type-4	C,Q	Macropain subunit PRE6, Multicatalytic endopeptidase complex subunit PRE6, Proteasome component PRE6, Proteinase YSCE subunit PRE6
	ec: 3.4.25.1

mol_id	molecule	chains	synonym
4	Proteasome subunit alpha type-5	D,R	Macropain subunit PUP2, Multicatalytic endopeptidase complex subunit PUP2, Proteasome component PUP2, Proteinase YSCE subunit PUP2
	ec: 3.4.25.1

mol_id	molecule	chains	synonym
5	Proteasome subunit alpha type-6	E,S	Macropain subunit PRE5, Multicatalytic endopeptidase complex subunit PRE5, Proteasome component PRE5, Proteinase YSCE subunit PRE5
	ec: 3.4.25.1

mol_id	molecule	chains	synonym
6	Probable proteasome subunit alpha type-7	F,T	Macropain subunit C1, Multicatalytic endopeptidase complex subunit C1, Proteasome component C1, Proteinase YSCE subunit 1
	ec: 3.4.25.1

mol_id	molecule	chains	synonym
7	Proteasome subunit alpha type-1	G,U	Macropain subunit C7-alpha, Multicatalytic endopeptidase complex C7, Proteasome component C7-alpha, Proteasome component Y8, Proteinase YSCE subunit 7, SCL1 suppressor protein
	ec: 3.4.25.1

mol_id	molecule	chains	synonym
8	Proteasome subunit beta type-2	H,V	Macropain subunit PUP1, Multicatalytic endopeptidase complex subunit PUP1, Proteasome component PUP1, Proteinase YSCE subunit PUP1
	ec: 3.4.25.1

mol_id	molecule	chains	synonym
9	Proteasome subunit beta type-3	I,W	Macropain subunit PUP3, Multicatalytic endopeptidase complex subunit PUP3, Proteasome component PUP3
	ec: 3.4.25.1

mol_id	molecule	chains	synonym
10	Proteasome subunit beta type-4	J,X	Macropain subunit C11, Multicatalytic endopeptidase complex subunit C11, Proteasome component C11, Proteinase YSCE subunit 11
	ec: 3.4.25.1

mol_id	molecule	chains	synonym
11	Proteasome subunit beta type-5	K,Y	Macropain subunit PRE2, Multicatalytic endopeptidase complex subunit PRE2, Proteasome component PRE2, Proteinase YSCE subunit PRE2
	ec: 3.4.25.1

mol_id	molecule	chains	synonym
12	Proteasome subunit beta type-6	L,Z	Multicatalytic endopeptidase complex subunit C5, Proteasome component C5
	ec: 3.4.25.1

mol_id	molecule	chains	synonym
13	Proteasome subunit beta type-7	M,a	Macropain subunit PRE4, Multicatalytic endopeptidase complex subunit PRE4, Proteasome component PRE4, Proteinase YSCE subunit PRE4
	ec: 3.4.25.1

mol_id	molecule	chains	synonym
14	Proteasome subunit beta type-1	N,b	Macropain subunit PRE3, Multicatalytic endopeptidase complex subunit PRE3, Proteasome component PRE3, Proteinase YSCE subunit PRE3
	ec: 3.4.25.1

mol_id	molecule	chains
15	TMC-95A mimic ligand yCP:4a fragment P	c

mol_id	molecule	chains
16	TMC-95A mimic ligand yCP:4a fragment Q	d

Source :

mol_id	organism_scientific	organism_common
1	Saccharomyces cerevisiae (taxid:559292)	Yeast
	strain: ATCC 204508 / S288c

mol_id	organism_scientific	organism_common
2	Saccharomyces cerevisiae (taxid:559292)	Yeast
	strain: ATCC 204508 / S288c

mol_id	organism_scientific	organism_common
3	Saccharomyces cerevisiae (taxid:559292)	Yeast
	strain: ATCC 204508 / S288c

mol_id	organism_scientific	organism_common
4	Saccharomyces cerevisiae (taxid:559292)	Yeast
	strain: ATCC 204508 / S288c

mol_id	organism_scientific	organism_common
5	Saccharomyces cerevisiae (taxid:559292)	Yeast
	strain: ATCC 204508 / S288c

mol_id	organism_scientific	organism_common
6	Saccharomyces cerevisiae (taxid:559292)	Yeast
	strain: ATCC 204508 / S288c

mol_id	organism_scientific	organism_common
7	Saccharomyces cerevisiae (taxid:559292)	Yeast
	strain: ATCC 204508 / S288c

mol_id	organism_scientific	organism_common
8	Saccharomyces cerevisiae (taxid:559292)	Yeast
	strain: ATCC 204508 / S288c

mol_id	organism_scientific	organism_common
9	Saccharomyces cerevisiae (taxid:559292)	Yeast
	strain: ATCC 204508 / S288c

mol_id	organism_scientific	organism_common
10	Saccharomyces cerevisiae (taxid:559292)	Yeast
	strain: ATCC 204508 / S288c

mol_id	organism_scientific	organism_common
11	Saccharomyces cerevisiae (taxid:559292)	Yeast
	strain: ATCC 204508 / S288c

mol_id	organism_scientific	organism_common
12	Saccharomyces cerevisiae (taxid:559292)	Yeast
	strain: ATCC 204508 / S288c

mol_id	organism_scientific	organism_common
13	Saccharomyces cerevisiae (taxid:559292)	Yeast
	strain: ATCC 204508 / S288c

mol_id	organism_scientific	organism_common
14	Saccharomyces cerevisiae (taxid:559292)	Yeast
	strain: ATCC 204508 / S288c

mol_id	organism_scientific
15
	synthetic: yes

mol_id	organism_scientific
16
	synthetic: yes

Authors :

Desvergne, A., Genin, E., Marechal, X., Gallastegui, N., Dufau, L., Richy, N., Groll, M., Vidal, J., Reboud-Ravaux, M.

Keywords :

UPS, proteasome, drug discovery, non-covalent reversible inhibition, bivalence, TMC-95A derivatives, Ntn hydrolase, non-lysosomal protein breakdown, HYDROLASE-HYDROLASE INHIBITOR complex

Exp. method :

X-RAY DIFFRACTION ( 3.10 Å )

Citation :

Dimerized linear mimics of a natural cyclopeptide (TMC-95A) are potent noncovalent inhibitors of the eukaryotic 20S proteasome.

Desvergne, A.,Genin, E.,Marechal, X. et al.
(2013) J.Med.Chem. 56 : 3367 - 3378

PubMed: 23540790
DOI: 10.1021/jm4002007

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: 4JT0

Hetero Atom Contents

Structure summary

Reaction