Het-PDB Navi2 (PDB: 4Y8H)

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Ligands
Code	Name	Link
CL	Chloride ion	PoSSuM
MES	2-(N-morpholino)-ethanesulfonic acid	PoSSuM
MG	Magnesium ion	PoSSuM

Non-standard Residues
Code	Name	Show

Glycosylation
Code	Name	Emphasize

Modification
Code	Name	Show
05W	(2r,3s,4s)-4-azanyl-2,6-dimethyl-heptane-1,3-diol
ACE	Acetyl group
AZI	Azide ion

Download interaction data: 4Y8H

Code :

4Y8H PDBj RCSB PDB PDBe

Header :

HYDROLASE/HYDROLASE INHIBITOR

Title :

Yeast 20S proteasome in complex with N3-APAL-ep

Release Data :

2015-06-17

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
11	PROTEASOME SUBUNIT BETA TYPE-5	K,Y

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	N3-APAL-ep	c,d,e,f,g,h

Source :

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Authors :

Huber, E.M., Groll, M.

Keywords :

HYDROLASE-HYDROLASE INHIBITOR complex, Proteasome, Inhibitor, Binding Analysis

Exp. method :

X-RAY DIFFRACTION ( 2.50 Å )

Citation :

Systematic Analyses of Substrate Preferences of 20S Proteasomes Using Peptidic Epoxyketone Inhibitors.

Huber, E.M.,de Bruin, G.,Heinemeyer, W. et al.
(2015) J.Am.Chem.Soc. 137 : 7835 - 7842

PubMed: 26020686
DOI: 10.1021/jacs.5b03688

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: 4Y8H

Hetero Atom Contents

Structure summary

Reaction