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- PDB-5l6c: Yeast 20S proteasome with mouse beta5i (1-138) and mouse beta6 (9... -

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Basic information

Entry
Database: PDB / ID: 5l6c
TitleYeast 20S proteasome with mouse beta5i (1-138) and mouse beta6 (97-111; 118-133) in complex with epoxyketone inhibitor 18
Components
  • (Proteasome subunit alpha type- ...) x 6
  • (Proteasome subunit beta type- ...) x 7
  • Probable proteasome subunit alpha type-7
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex / Proteasome / Mutant / Inhibitor / Binding Analysis
Function / homology
Function and homology information


Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / Assembly of the pre-replicative complex ...Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M Checkpoints / Degradation of AXIN / Asymmetric localization of PCP proteins / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Regulation of RUNX3 expression and activity / Regulation of RAS by GAPs / Regulation of PTEN stability and activity / Regulation of RUNX2 expression and activity / Degradation of GLI1 by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / spermatoproteasome complex / Degradation of DVL / UCH proteinases / Orc1 removal from chromatin / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / Hedgehog ligand biogenesis / TNFR2 non-canonical NF-kB pathway / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Hedgehog 'on' state / Degradation of beta-catenin by the destruction complex / Activation of NF-kappaB in B cells / The role of GTSE1 in G2/M progression after G2 checkpoint / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Separation of Sister Chromatids / Downstream TCR signaling / MAPK6/MAPK4 signaling / KEAP1-NFE2L2 pathway / GLI3 is processed to GLI3R by the proteasome / ABC-family proteins mediated transport / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / proteasome core complex / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Orc1 removal from chromatin / fat cell differentiation / MAPK6/MAPK4 signaling / proteasome storage granule / antigen processing and presentation / Antigen processing: Ubiquitination & Proteasome degradation / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / Ub-specific processing proteases / threonine-type endopeptidase activity / Neutrophil degranulation / Neutrophil degranulation / proteasome complex / proteolysis involved in protein catabolic process / peroxisome / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. ...Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6NV / Proteasome subunit beta type-1 / Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 ...Chem-6NV / Proteasome subunit beta type-1 / Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-8 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4
Similarity search - Component
Biological speciesMus musculus (house mouse)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGroll, M. / Huber, E.M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationGR1861/10-1 Germany
CitationJournal: EMBO J. / Year: 2016
Title: A humanized yeast proteasome identifies unique binding modes of inhibitors for the immunosubunit beta 5i.
Authors: Huber, E.M. / Heinemeyer, W. / de Bruin, G. / Overkleeft, H.S. / Groll, M.
History
DepositionMay 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome subunit alpha type-2
B: Proteasome subunit alpha type-3
C: Proteasome subunit alpha type-4
D: Proteasome subunit alpha type-5
E: Proteasome subunit alpha type-6
F: Probable proteasome subunit alpha type-7
G: Proteasome subunit alpha type-1
H: Proteasome subunit beta type-2
I: Proteasome subunit beta type-3
J: Proteasome subunit beta type-4
K: Proteasome subunit beta type-8,Proteasome subunit beta type-5
L: Proteasome subunit beta type-6,Proteasome subunit beta type-1,Proteasome subunit beta type-6,Proteasome subunit beta type-1,Proteasome subunit beta type-6
M: Proteasome subunit beta type-7
N: Proteasome subunit beta type-1
O: Proteasome subunit alpha type-2
P: Proteasome subunit alpha type-3
Q: Proteasome subunit alpha type-4
R: Proteasome subunit alpha type-5
S: Proteasome subunit alpha type-6
T: Probable proteasome subunit alpha type-7
U: Proteasome subunit alpha type-1
V: Proteasome subunit beta type-2
W: Proteasome subunit beta type-3
X: Proteasome subunit beta type-4
Y: Proteasome subunit beta type-8,Proteasome subunit beta type-5
Z: Proteasome subunit beta type-6,Proteasome subunit beta type-1,Proteasome subunit beta type-6,Proteasome subunit beta type-1,Proteasome subunit beta type-6
a: Proteasome subunit beta type-7
b: Proteasome subunit beta type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)733,15541
Polymers731,46728
Non-polymers1,68813
Water8,683482
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.570, 300.640, 145.790
Angle α, β, γ (deg.)90.00, 112.87, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21O
12B
22P
13C
23Q
14D
24R
15E
25S
16F
26T
17G
27U
18H
28V
19I
29W
110J
210X
111K
211Y
112L
212Z
113M
213a
114N
214b

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 300
2111O1 - 300
1121B1 - 300
2121P1 - 300
1131C1 - 300
2131Q1 - 300
1141D1 - 300
2141R1 - 300
1151E1 - 300
2151S1 - 300
1161F1 - 300
2161T1 - 300
1171G1 - 300
2171U1 - 300
1181H1 - 300
2181V1 - 300
1191I1 - 300
2191W1 - 300
11101J1 - 300
21101X1 - 300
11111K1 - 300
21111Y1 - 300
11121L1 - 300
21121Z1 - 300
11131M1 - 300
21131a1 - 300
11141N1 - 300
21141b1 - 300

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999595, -0.00024, 0.028459), (-0.004754, -0.984509, -0.175267), (0.02806, -0.175331, 0.98411)67.74332, -289.07492, -26.67216

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Components

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Proteasome subunit alpha type- ... , 6 types, 12 molecules AOBPCQDRESGU

#1: Protein Proteasome subunit alpha type-2 / Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteasome component Y7 / ...Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteasome component Y7 / Proteinase YSCE subunit 7


Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P23639, proteasome endopeptidase complex
#2: Protein Proteasome subunit alpha type-3 / Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteasome component Y13 ...Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteasome component Y13 / Proteinase YSCE subunit 13


Mass: 28748.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P23638, proteasome endopeptidase complex
#3: Protein Proteasome subunit alpha type-4 / Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteasome component ...Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteasome component PRE6 / Proteinase YSCE subunit PRE6


Mass: 28478.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P40303, proteasome endopeptidase complex
#4: Protein Proteasome subunit alpha type-5 / Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteasome component ...Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteasome component PUP2 / Proteinase YSCE subunit PUP2


Mass: 28649.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P32379, proteasome endopeptidase complex
#5: Protein Proteasome subunit alpha type-6 / Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteasome component ...Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteasome component PRE5 / Proteinase YSCE subunit PRE5


Mass: 25634.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P40302, proteasome endopeptidase complex
#7: Protein Proteasome subunit alpha type-1 / Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component C7- ...Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component C7-alpha / Proteasome component Y8 / Proteinase YSCE subunit 7 / SCL1 suppressor protein


Mass: 28033.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P21243, proteasome endopeptidase complex

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Protein , 1 types, 2 molecules FT

#6: Protein Probable proteasome subunit alpha type-7 / Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteasome component C1 / ...Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteasome component C1 / Proteinase YSCE subunit 1


Mass: 31575.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P21242, proteasome endopeptidase complex

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Proteasome subunit beta type- ... , 7 types, 14 molecules HVIWJXKYLZMaNb

#8: Protein Proteasome subunit beta type-2 / Macropain subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1 / Proteasome component ...Macropain subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1 / Proteasome component PUP1 / Proteinase YSCE subunit PUP1


Mass: 25114.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P25043, proteasome endopeptidase complex
#9: Protein Proteasome subunit beta type-3 / Macropain subunit PUP3 / Multicatalytic endopeptidase complex subunit PUP3 / Proteasome component PUP3


Mass: 22627.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P25451, proteasome endopeptidase complex
#10: Protein Proteasome subunit beta type-4 / Macropain subunit C11 / Multicatalytic endopeptidase complex subunit C11 / Proteasome component C11 ...Macropain subunit C11 / Multicatalytic endopeptidase complex subunit C11 / Proteasome component C11 / Proteinase YSCE subunit 11


Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P22141, proteasome endopeptidase complex
#11: Protein Proteasome subunit beta type-8,Proteasome subunit beta type-5 / Low molecular mass protein 7 / Macropain subunit C13 / Multicatalytic endopeptidase complex subunit ...Low molecular mass protein 7 / Macropain subunit C13 / Multicatalytic endopeptidase complex subunit C13 / Proteasome component C13 / Proteasome subunit beta-5i / Macropain subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2 / Proteasome component PRE2 / Proteinase YSCE subunit PRE2


Mass: 23438.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: Psmb8, Lmp7, Mc13, PRE2, DOA3, PRG1, YPR103W, P8283.10
Strain: ATCC 204508 / S288c
Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P28063, UniProt: P30656, proteasome endopeptidase complex
#12: Protein Proteasome subunit beta type-6,Proteasome subunit beta type-1,Proteasome subunit beta type-6,Proteasome subunit beta type-1,Proteasome subunit beta type-6 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Macropain subunit C5 / ...Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Proteasome gamma chain / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Proteasome gamma chain / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5


Mass: 24979.010 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) Mus musculus (house mouse), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: PRE7, PRS3, PTS1, YBL041W, YBL0407, Psmb1
Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P23724, UniProt: O09061, proteasome endopeptidase complex
#13: Protein Proteasome subunit beta type-7 / Macropain subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4 / Proteasome component ...Macropain subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4 / Proteasome component PRE4 / Proteinase YSCE subunit PRE4


Mass: 27200.893 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P30657, proteasome endopeptidase complex
#14: Protein Proteasome subunit beta type-1 / Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component ...Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component PRE3 / Proteinase YSCE subunit PRE3


Mass: 21517.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P38624, proteasome endopeptidase complex

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Non-polymers , 5 types, 495 molecules

#15: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#16: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#17: Chemical 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


Mass: 613.743 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C36H43N3O6
#18: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#19: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.67 Å3/Da / Density % sol: 66.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 20 mM MgAC2, 13% MPD, 0.1 M MES / PH range: 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2015
RadiationMonochromator: LN2 COOLED FIXED-EXIT. SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 317147 / % possible obs: 96.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 12.7
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 2.5 / % possible all: 98.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMAC5.7.0032refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CZ4

5cz4


Resolution: 2.6→15 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 21.039 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R Free: 0.237 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21735 15858 5 %RANDOM
Rwork0.19213 ---
obs0.19339 301289 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 63.833 Å2
Baniso -1Baniso -2Baniso -3
1-3.5 Å20 Å2-0.84 Å2
2---5.35 Å2-0 Å2
3---1.63 Å2
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49392 0 112 482 49986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01950418
X-RAY DIFFRACTIONr_bond_other_d0.0010.0248152
X-RAY DIFFRACTIONr_angle_refined_deg0.8791.96668209
X-RAY DIFFRACTIONr_angle_other_deg0.7333.001110871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.82956316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.2124.3892258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.114158778
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2715289
X-RAY DIFFRACTIONr_chiral_restr0.0490.27664
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0257235
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0211326
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1855.39625342
X-RAY DIFFRACTIONr_mcbond_other2.1855.39625341
X-RAY DIFFRACTIONr_mcangle_it2.8728.07831626
X-RAY DIFFRACTIONr_mcangle_other2.8728.07831627
X-RAY DIFFRACTIONr_scbond_it2.1715.84225076
X-RAY DIFFRACTIONr_scbond_other2.1715.84225076
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.638.59536582
X-RAY DIFFRACTIONr_long_range_B_refined3.37142.39554187
X-RAY DIFFRACTIONr_long_range_B_other3.34242.38954134
X-RAY DIFFRACTIONr_rigid_bond_restr0.813398570
X-RAY DIFFRACTIONr_sphericity_free34.6895307
X-RAY DIFFRACTIONr_sphericity_bonded13.766597846
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3099TIGHT POSITIONAL0.020.05
1A3278TIGHT POSITIONAL0.040.05
1A3449TIGHT POSITIONAL0.020.05
1A3598TIGHT POSITIONAL00.05
1A2949TIGHT POSITIONAL00.05
1A3795TIGHT THERMAL4.260.5
2B3756TIGHT THERMAL3.30.5
3C3729TIGHT THERMAL7.890.5
4D3578TIGHT THERMAL7.350.5
5E3509TIGHT THERMAL4.920.5
6F3749TIGHT THERMAL6.120.5
7G3770TIGHT THERMAL3.760.5
8H3389TIGHT THERMAL3.230.5
9I3119TIGHT THERMAL2.570.5
10J3099TIGHT THERMAL2.860.5
11K3278TIGHT THERMAL2.620.5
12L3449TIGHT THERMAL3.250.5
13M3598TIGHT THERMAL2.750.5
14N2949TIGHT THERMAL1.930.5
LS refinement shellResolution: 2.6→2.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 1160 -
Rwork0.326 22028 -
obs--98.46 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.02430.00890.01310.00510.00470.011-0.01030.01550.0060.00190.003-0.0095-0.0159-0.00570.00730.1135-0.0074-0.00010.0764-0.00470.114866.9338-92.141846.3569
20.02090.0080.00630.00650.00620.0075-0.0187-0.0003-0-0.02150.00340.0097-0.01860.01160.01520.1139-0.00150.01630.0803-0.00090.105959.6374-87.913516.6566
30.07420.0422-0.05170.0252-0.03010.0366-0.0034-0.00150.0041-0.00020.00930.0106-0.0005-0.0005-0.00590.13310.0015-0.0090.07650.00950.109532.2899-87.54581.4181
40.0037-0.0047-0.0070.01220.00750.01450.0045-0.0078-0.0047-0.02220.00110.0276-0.02060.0117-0.00550.0910.0207-0.010.03770.01640.11273.0504-89.984313.9812
50.03470.00510.02030.01360.00240.0120.01140.0008-0.00820.0117-0.00430.03730.00550.0022-0.00710.08110.01960.01430.07090.00050.1229-3.192-94.401646.0119
60.031-0.0191-0.03060.01670.02070.0310.007-0.00730.00510.0126-0.00740.004-0.00060.00420.00050.11460.0050.01720.0686-0.00960.106115.2458-95.05170.2251
70.00840.0053-0.00360.012-0.00260.00160.00540.0207-0.00460.036-0.0032-0.0136-0.0049-0.0085-0.00220.1386-0.0007-0.00230.0606-0.00450.100647.7202-93.53471.4623
80.00390.003-0.00120.02130.01160.01280.020.0059-0.00110.0225-0.0059-0.04130.0075-0.0227-0.01410.1106-0.00180.00010.0574-0.01140.116367.7827-129.587247.7818
90.0015-0.0067-0.00580.18740.06710.05340.00320.0070.0011-0.0185-0.0043-0.0219-0.02440.01010.00110.1117-0.00130.00840.0807-0.00010.115668.4451-127.433321.2015
100.0305-0.00830.00370.0566-0.00520.0015-0.00080.00060.0024-0.02780.00280.00040.0080.005-0.0020.1367-0.0005-0.00210.07670.00020.105644.5617-126.6486-0.0846
110.00220.0036-0.00110.0126-0.00020.0011-0.0074-0.00520.0098-0.03650.00650.01730.00140.00680.00080.11770.0005-0.02040.04490.00570.121610.6887-130.9563.2573
120.02880.04290.05230.07250.07710.11050.00950.0063-0.00150.0047-0.0060.0197-0.00510.0331-0.00340.10930.0063-0.00690.06560.01180.1296-4.5162-134.364828.8598
130.016-0.04730.00730.2124-0.0280.00430.00470.01320.00830.0437-0.00320.0235-0.00590.0068-0.00150.1206-0.00260.00940.0643-0.00410.10877.779-137.90360.7435
140.0307-0.0079-0.01280.10850.03360.01520.021-0.0051-0.00590.0174-0.01240.0067-0.0004-0.0036-0.00860.1329-0.00670.00050.0682-0.00430.100239.8407-134.1171.2043
150.0055-0.0075-0.00360.0530.01840.0104-0.0060.01730.0048-0.0018-0.00150.01770.0213-0.00180.00750.1225-0.0091-0.01410.07320.00180.11521.9213-206.686837.3296
160.03010.01760.00520.01140.00250.0024-0.00640.0104-0.0022-0.010100.00440.00660.00670.00640.1288-0.0073-0.01980.0694-0.00430.11478.4324-205.72657.1161
170.0055-0.00220.01790.0024-0.01180.09930.0082-0.0120.0034-0.01270.00780.00560.0113-0.006-0.0160.13860.0041-0.01220.0678-0.00370.095735.5131-203.6186-8.649
180.0171-0.02040.00430.0271-0.00670.00240.0058-0.01030.034-0.0258-0.0042-0.04340.01190.0034-0.00160.06820.02930.01770.0347-0.02530.082965.029-203.27373.4325
190.0007-0.0001-0.00070.00640.00390.00340.00830.00320.00540.01590.0077-0.02340.0056-0.0024-0.01590.08790.0301-0.01670.03360.00150.122772.0747-204.321835.5329
200.02760.0080.00860.00350.00320.00450.0274-0.017-0.01430.0083-0.0145-0.0140.0011-0.0126-0.01290.13970.014-0.03530.03940.01680.10254.1867-207.883359.9307
210.0055-0.00560.01120.0121-0.01640.0325-0.00330.0115-0.00040.00960.00270.01580.00190.00610.00060.14620.0004-0.01530.06170.00710.099321.7881-209.850361.6439
220.00270.00580.00180.01350.00260.00390.01020.00260.00910.0293-0.00410.02380.01350.0127-0.00610.11810.0006-0.00780.06950.010.10831.2467-170.098645.1926
230.0026-0.0012-0.00060.0031-0.00010.00060.00750.0135-0.0006-0.0013-0.00470.01790.0047-0.0051-0.00280.11880.0012-0.0110.08160.00660.124-0.0368-167.652918.5894
240.0065-0.0023-0.00490.00140.00270.00580.0174-0.0110.0086-0.0119-0.0023-0.0046-0.0205-0.0018-0.01510.14450.0076-0.02040.07040.00240.107423.3333-164.7209-3.1191
250.0024-0.00030.00260.0047-0.00030.0030.0019-0.0034-0.0155-0.01920.0123-0.00530-0.0008-0.01420.120.00860.02520.0544-0.01020.12357.2788-160.9910.0496
260.01130.0163-0.00860.0298-0.00970.01720.01640.001-0.00610.0158-0.0054-0.034-0.002-0.0199-0.0110.11160.00890.00150.0686-0.01160.13273.0724-162.041225.4542
270.0157-0.0151-00.0584-0.00110.00330.0190.0193-0.01640.0205-0.0125-0.01090.0081-0.0104-0.00650.1280.004-0.0080.05740.00170.118661.5612-164.020257.787
280.00190.0104-0.00240.1219-0.0510.02560.00980.002-0.00640.0352-0.0002-0.00020.00140.0079-0.00960.1316-0.00450.00440.06760.00220.099829.7735-169.61868.3157
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 250
2X-RAY DIFFRACTION2B1 - 244
3X-RAY DIFFRACTION3C1 - 240
4X-RAY DIFFRACTION4D1 - 242
5X-RAY DIFFRACTION5E3 - 233
6X-RAY DIFFRACTION6F2 - 244
7X-RAY DIFFRACTION7G2 - 242
8X-RAY DIFFRACTION8H1 - 226
9X-RAY DIFFRACTION9I1 - 204
10X-RAY DIFFRACTION10J1 - 195
11X-RAY DIFFRACTION11K1 - 211
12X-RAY DIFFRACTION12L1 - 222
13X-RAY DIFFRACTION13M1 - 233
14X-RAY DIFFRACTION14N1 - 196
15X-RAY DIFFRACTION15O1 - 250
16X-RAY DIFFRACTION16P1 - 244
17X-RAY DIFFRACTION17Q1 - 240
18X-RAY DIFFRACTION18R1 - 242
19X-RAY DIFFRACTION19S3 - 233
20X-RAY DIFFRACTION20T2 - 244
21X-RAY DIFFRACTION21U2 - 242
22X-RAY DIFFRACTION22V1 - 226
23X-RAY DIFFRACTION23W1 - 204
24X-RAY DIFFRACTION24X1 - 195
25X-RAY DIFFRACTION25Y1 - 211
26X-RAY DIFFRACTION26Z1 - 222
27X-RAY DIFFRACTION27a1 - 233
28X-RAY DIFFRACTION28b1 - 196

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