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Structure paper

TitleA humanized yeast proteasome identifies unique binding modes of inhibitors for the immunosubunit beta 5i.
Journal, issue, pagesEMBO J., Vol. 35, Page 2602-2613, Year 2016
Publish dateMay 27, 2016 (structure data deposition date)
AuthorsHuber, E.M. / Heinemeyer, W. / de Bruin, G. / Overkleeft, H.S. / Groll, M.
External linksEMBO J. / PubMed:27789522
MethodsX-ray diffraction
Resolution2.4 - 2.9 Å
Structure data

PDB-5l52:
Yeast 20S proteasome in complex with epoxyketone inhibitor 14
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-5l54:
Yeast 20S proteasome in complex with epoxyketone inhibitor 16
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-5l55:
Yeast 20S proteasome in complex with epoxyketone inhibitor 18
Method: X-RAY DIFFRACTION / Resolution: 2.9 Å

PDB-5l5a:
Yeast 20S proteasome with human beta5i (1-138; R57T)
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

PDB-5l5b:
Yeast 20S proteasome with human beta5i (1-138) and human beta6 (97-111; 118-133)
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-5l5d:
Yeast 20S proteasome with human beta5i (1-138) and human beta6 (97-111; 118-133) in complex with ONX 0914
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-5l5e:
Yeast 20S proteasome with human beta5i (1-138) and human beta6 (97-111; 118-133) in complex with carfilzomib
Method: X-RAY DIFFRACTION / Resolution: 2.9 Å

PDB-5l5f:
Yeast 20S proteasome with human beta5i (1-138) and human beta6 (97-111; 118-133) in complex with bortezomib
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

PDB-5l5h:
Yeast 20S proteasome with human beta5i (1-138) and human beta6 (97-111; 118-133) in complex with PR-924
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-5l5i:
Yeast 20S proteasome with human beta5i (1-138) and human beta6 (97-111; 118-133) in complex with epoxyketone inhibitor 9
Method: X-RAY DIFFRACTION / Resolution: 2.9 Å

PDB-5l5j:
Yeast 20S proteasome with human beta5i (1-138) and human beta6 (97-111; 118-133) in complex with epoxyketone inhibitor 14
Method: X-RAY DIFFRACTION / Resolution: 2.9 Å

PDB-5l5o:
Yeast 20S proteasome with human beta5i (1-138) and human beta6 (97-111; 118-133) in complex with epoxyketone inhibitor 16
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-5l5p:
Yeast 20S proteasome with human beta5i (1-138) and human beta6 (97-111; 118-133) in complex with epoxyketone inhibitor 17
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-5l5q:
Yeast 20S proteasome with human beta5i (1-138) and human beta6 (97-111; 118-133) in complex with epoxyketone 18
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-5l5r:
Yeast 20S proteasome with human beta5i (1-138;V31M) and human beta6 (97-111; 118-133)
Method: X-RAY DIFFRACTION / Resolution: 2.9 Å

PDB-5l5s:
Yeast 20S proteasome with human beta5i (1-138; V31M) and human beta6 (97-111; 118-133) in complex with PR-924
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-5l5t:
Yeast 20S proteasome with human beta5i (1-138; V31M) and human beta6 (97-111; 118-133) in complex with epoxyketone inhibitor 16
Method: X-RAY DIFFRACTION / Resolution: 2.9 Å

PDB-5l5u:
Yeast 20S proteasome with human beta5i (1-138; V31M) and human beta6 (97-111; 118-133) in complex with epoxyketone inhibitor 17
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-5l5v:
'Yeast 20S proteasome with human beta5i (1-138; V31M) and human beta6 (97-111; 118-133) in complex with epoxyketone inhibitor 18
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-5l5w:
Yeast 20S proteasome with human beta5c (1-138) and human beta6 (97-111; 118-133)
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-5l5x:
Yeast 20S proteasome with human beta5c (1-138) and human beta6 (97-111; 118-133) in complex with ONX 0914
Method: X-RAY DIFFRACTION / Resolution: 2.9 Å

PDB-5l5y:
Yeast 20S proteasome with human beta5c (1-138) and human beta6 (97-111; 118-133) in complex with carfilzomib
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-5l5z:
Yeast 20S proteasome with human beta5c (1-138) and human beta6 (97-111; 118-133) in complex with bortezomib
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-5l60:
Yeast 20S proteasome with human beta5c (1-138) and human beta6 (97-111; 118-133) in complex with PR-924
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-5l61:
Yeast 20S proteasome with human beta5c (1-138) and human beta6 (99-132) in complex with epoxyketone inhibitor 14
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-5l62:
Yeast 20S proteasome with human beta5c (1-138) and human beta6 (97-111; 118-133) in complex with epoxyketone inhibitor 16
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-5l63:
Yeast 20S proteasome with human beta5c (1-138) and human beta6 (97-111; 118-133) in complex with epoxyketone inhibitor 17
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-5l64:
Yeast 20S proteasome with human beta5c (1-138) and human beta6 (97-111; 118-133) in complex with epoxyketone inhibitor 18
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-5l65:
Yeast 20S proteasome with mouse beta5i (1-138) and mouse beta6 (97-111; 118-133) in complex with carfilzomib
Method: X-RAY DIFFRACTION / Resolution: 2.9 Å

PDB-5l66:
Yeast 20S proteasome with mouse beta5i (1-138) and mouse beta6 (97-111; 118-133) in complex with bortezomib
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-5l67:
Yeast 20S proteasome with mouse beta5i (1-138) and mouse beta6 (97-111; 118-133) in complex with PR-924
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-5l68:
Yeast 20S proteasome with mouse beta5i (1-138) and mouse beta6 (97-111; 118-133) in complex with epoxyketone inhibitor 14
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-5l69:
Yeast 20S proteasome with mouse beta5i (1-138) and mouse beta6 (97-111; 118-133) in complex with epoxyketone inhibitor 16
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-5l6a:
Yeast 20S proteasome with mouse beta5i (1-138) and mouse beta6 (97-111; 118-133) in complex with epoxyketone inhibitor 17
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-5l6b:
Yeast 20S proteasome with mouse beta5i (1-138) and mouse beta6 (97-111; 118-133) in complex with ONX 0914
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-5l6c:
Yeast 20S proteasome with mouse beta5i (1-138) and mouse beta6 (97-111; 118-133) in complex with epoxyketone inhibitor 18
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-5ltt:
Yeast 20S proteasome with human beta5i (1-138; R57T)in complex with PR-924
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-CL:
Unknown entry / Chloride

ChemComp-6N5:
~{N}-[(2~{S})-1-[[(2~{S})-3-(4-methoxyphenyl)-1-[[(2~{S},3~{S},4~{R})-4-methyl-3,5-bis(oxidanyl)-1-phenyl-pentan-2-yl]amino]-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-propan-2-yl]-1-methyl-5~{H}-indene-2-carboxamide

ChemComp-MES:
2-(N-MORPHOLINO)-ETHANESULFONIC ACID / pH buffer*YM / MES (buffer)

ChemComp-HOH:
WATER / Water

ChemComp-79P:
(2~{S})-3-(1~{H}-indol-3-yl)-~{N}-[(2~{S},3~{S},4~{R})-4-methyl-3,5-bis(oxidanyl)-1-phenyl-pentan-2-yl]-2-[[(2~{R})-2-(2-morpholin-4-ylethanoylamino)propanoyl]amino]propanamide

ChemComp-6NV:
~{N}-[(2~{R})-1-[[(2~{S})-3-(4-methoxyphenyl)-1-[[(2~{S},3~{S},4~{R})-4-methyl-3,5-bis(oxidanyl)-1-phenyl-pentan-2-yl]amino]-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-propan-2-yl]-1-methyl-5~{H}-indene-2-carboxamide

ChemComp-04C:
1,2,4-trideoxy-4-methyl-2-{[N-(morpholin-4-ylacetyl)-L-alanyl-O-methyl-L-tyrosyl]amino}-1-phenyl-D-xylitol

ChemComp-3BV:
N-{(2S)-2-[(morpholin-4-ylacetyl)amino]-4-phenylbutanoyl}-L-leucyl-N-[(2R,3S,4S)-1,3-dihydroxy-2,6-dimethylheptan-4-yl]-L-phenylalaninamide / medication, anticancer, inhibitor*YM / Carfilzomib

ChemComp-BO2:
N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE / medication, anticancer*YM / Bortezomib

ChemComp-39V:
N-[(3-methyl-1H-inden-2-yl)carbonyl]-D-alanyl-N-[(2S,4R)-5-hydroxy-4-methyl-3-oxo-1-phenylpentan-2-yl]-L-tryptophanamide

ChemComp-38X:
N-[(3-methyl-1H-inden-2-yl)carbonyl]-D-alanyl-N-[(2S,4R)-1-cyclohexyl-5-hydroxy-4-methyl-3-oxopentan-2-yl]-L-tryptophanamide

ChemComp-79L:
(2~{S})-3-(4-methoxyphenyl)-~{N}-[(2~{S},3~{S},4~{R})-4-methyl-3,5-bis(oxidanyl)-1-phenyl-pentan-2-yl]-2-[[(2~{R})-2-(2-morpholin-4-ylethanoylamino)propanoyl]amino]propanamide

Source
  • saccharomyces cerevisiae s288c (yeast)
  • saccharomyces cerevisiae (strain atcc 204508 / s288c) (yeast)
  • homo sapiens (human)
  • saccharomyces cerevisiae (brewer's yeast)
  • mus musculus (house mouse)
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex / Proteasome / Inhibitor / Binding Analysis / HYDROLASE complex / Mutant

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