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- PDB-6v8w: CDYL2 chromodomain in complex with a synthetic peptide -

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Basic information

Entry
Database: PDB / ID: 6v8w
TitleCDYL2 chromodomain in complex with a synthetic peptide
Components
  • Chromodomain Y-like protein 2
  • IVA-PHE-ALA-PHE-5T3-SER-NH2
KeywordsPROTEIN BINDING / chromodomain / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


methylated histone binding / transcription corepressor activity / nucleus
Similarity search - Function
Chromo domain, conserved site / Chromo domain signature. / Enoyl-CoA hydratase, C-terminal / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase ...Chromo domain, conserved site / Chromo domain signature. / Enoyl-CoA hydratase, C-terminal / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / Chromo-like domain superfamily / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
Chromodomain Y-like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDong, C. / Tempel, W. / James, L.I. / Lamb, K.N. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Min, J. / Structural Genomics Consortium / Structural Genomics Consortium (SGC)
CitationJournal: Cell Chem Biol / Year: 2020
Title: Structural Basis for the Binding Selectivity of Human CDY Chromodomains.
Authors: Dong, C. / Liu, Y. / Lyu, T.J. / Beldar, S. / Lamb, K.N. / Tempel, W. / Li, Y. / Li, Z. / James, L.I. / Qin, S. / Wang, Y. / Min, J.
History
DepositionDec 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromodomain Y-like protein 2
AA: IVA-PHE-ALA-PHE-5T3-SER-NH2
B: Chromodomain Y-like protein 2
BB: IVA-PHE-ALA-PHE-5T3-SER-NH2
C: Chromodomain Y-like protein 2
CC: IVA-PHE-ALA-PHE-5T3-SER-NH2
D: Chromodomain Y-like protein 2
DD: IVA-PHE-ALA-PHE-5T3-SER-NH2
E: Chromodomain Y-like protein 2
EE: IVA-PHE-ALA-PHE-5T3-SER-NH2
F: Chromodomain Y-like protein 2
FF: IVA-PHE-ALA-PHE-5T3-SER-NH2
G: Chromodomain Y-like protein 2
GG: IVA-PHE-ALA-PHE-5T3-SER-NH2
H: Chromodomain Y-like protein 2
HH: IVA-PHE-ALA-PHE-5T3-SER-NH2
I: Chromodomain Y-like protein 2
II: IVA-PHE-ALA-PHE-5T3-SER-NH2
J: Chromodomain Y-like protein 2
JJ: IVA-PHE-ALA-PHE-5T3-SER-NH2
K: Chromodomain Y-like protein 2
KK: IVA-PHE-ALA-PHE-5T3-SER-NH2
L: Chromodomain Y-like protein 2
LL: IVA-PHE-ALA-PHE-5T3-SER-NH2
M: Chromodomain Y-like protein 2
MM: IVA-PHE-ALA-PHE-5T3-SER-NH2
N: Chromodomain Y-like protein 2
NN: IVA-PHE-ALA-PHE-5T3-SER-NH2
O: Chromodomain Y-like protein 2
OO: IVA-PHE-ALA-PHE-5T3-SER-NH2
P: Chromodomain Y-like protein 2
PP: IVA-PHE-ALA-PHE-5T3-SER-NH2
Q: Chromodomain Y-like protein 2
QQ: IVA-PHE-ALA-PHE-5T3-SER-NH2
R: Chromodomain Y-like protein 2
RR: IVA-PHE-ALA-PHE-5T3-SER-NH2
S: Chromodomain Y-like protein 2
SS: IVA-PHE-ALA-PHE-5T3-SER-NH2
T: Chromodomain Y-like protein 2
TT: IVA-PHE-ALA-PHE-5T3-SER-NH2
U: Chromodomain Y-like protein 2
UU: IVA-PHE-ALA-PHE-5T3-SER-NH2
V: Chromodomain Y-like protein 2
VV: IVA-PHE-ALA-PHE-5T3-SER-NH2
W: Chromodomain Y-like protein 2
WW: IVA-PHE-ALA-PHE-5T3-SER-NH2
X: Chromodomain Y-like protein 2
XX: IVA-PHE-ALA-PHE-5T3-SER-NH2
Y: Chromodomain Y-like protein 2
YY: IVA-PHE-ALA-PHE-5T3-SER-NH2
Z: Chromodomain Y-like protein 2
ZZ: IVA-PHE-ALA-PHE-5T3-SER-NH2


Theoretical massNumber of molelcules
Total (without water)213,25980
Polymers213,25952
Non-polymers028
Water0
1
A: Chromodomain Y-like protein 2
AA: IVA-PHE-ALA-PHE-5T3-SER-NH2


Theoretical massNumber of molelcules
Total (without water)8,2025
Polymers8,2022
Non-polymers03
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chromodomain Y-like protein 2
BB: IVA-PHE-ALA-PHE-5T3-SER-NH2


  • defined by author
  • 8.2 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)8,2022
Polymers8,2022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Chromodomain Y-like protein 2
CC: IVA-PHE-ALA-PHE-5T3-SER-NH2


Theoretical massNumber of molelcules
Total (without water)8,2024
Polymers8,2022
Non-polymers02
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Chromodomain Y-like protein 2
DD: IVA-PHE-ALA-PHE-5T3-SER-NH2


Theoretical massNumber of molelcules
Total (without water)8,2024
Polymers8,2022
Non-polymers02
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Chromodomain Y-like protein 2
EE: IVA-PHE-ALA-PHE-5T3-SER-NH2


Theoretical massNumber of molelcules
Total (without water)8,2022
Polymers8,2022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Chromodomain Y-like protein 2
FF: IVA-PHE-ALA-PHE-5T3-SER-NH2


Theoretical massNumber of molelcules
Total (without water)8,2026
Polymers8,2022
Non-polymers04
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Chromodomain Y-like protein 2
GG: IVA-PHE-ALA-PHE-5T3-SER-NH2


  • defined by author
  • 8.2 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)8,2023
Polymers8,2022
Non-polymers01
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Chromodomain Y-like protein 2
HH: IVA-PHE-ALA-PHE-5T3-SER-NH2


Theoretical massNumber of molelcules
Total (without water)8,2023
Polymers8,2022
Non-polymers01
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Chromodomain Y-like protein 2
II: IVA-PHE-ALA-PHE-5T3-SER-NH2


  • defined by author
  • 8.2 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)8,2023
Polymers8,2022
Non-polymers01
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Chromodomain Y-like protein 2
JJ: IVA-PHE-ALA-PHE-5T3-SER-NH2


Theoretical massNumber of molelcules
Total (without water)8,2023
Polymers8,2022
Non-polymers01
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Chromodomain Y-like protein 2
KK: IVA-PHE-ALA-PHE-5T3-SER-NH2


Theoretical massNumber of molelcules
Total (without water)8,2023
Polymers8,2022
Non-polymers01
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Chromodomain Y-like protein 2
LL: IVA-PHE-ALA-PHE-5T3-SER-NH2


Theoretical massNumber of molelcules
Total (without water)8,2022
Polymers8,2022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
M: Chromodomain Y-like protein 2
MM: IVA-PHE-ALA-PHE-5T3-SER-NH2


Theoretical massNumber of molelcules
Total (without water)8,2023
Polymers8,2022
Non-polymers01
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
N: Chromodomain Y-like protein 2
NN: IVA-PHE-ALA-PHE-5T3-SER-NH2


  • defined by author
  • 8.2 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)8,2024
Polymers8,2022
Non-polymers02
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
O: Chromodomain Y-like protein 2
OO: IVA-PHE-ALA-PHE-5T3-SER-NH2


  • defined by author
  • 8.2 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)8,2023
Polymers8,2022
Non-polymers01
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
16
P: Chromodomain Y-like protein 2
PP: IVA-PHE-ALA-PHE-5T3-SER-NH2


Theoretical massNumber of molelcules
Total (without water)8,2022
Polymers8,2022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
17
Q: Chromodomain Y-like protein 2
QQ: IVA-PHE-ALA-PHE-5T3-SER-NH2


Theoretical massNumber of molelcules
Total (without water)8,2023
Polymers8,2022
Non-polymers01
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
18
R: Chromodomain Y-like protein 2
RR: IVA-PHE-ALA-PHE-5T3-SER-NH2


  • defined by author
  • 8.2 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)8,2022
Polymers8,2022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
19
S: Chromodomain Y-like protein 2
SS: IVA-PHE-ALA-PHE-5T3-SER-NH2


Theoretical massNumber of molelcules
Total (without water)8,2025
Polymers8,2022
Non-polymers03
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
20
T: Chromodomain Y-like protein 2
TT: IVA-PHE-ALA-PHE-5T3-SER-NH2


Theoretical massNumber of molelcules
Total (without water)8,2023
Polymers8,2022
Non-polymers01
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
21
U: Chromodomain Y-like protein 2
UU: IVA-PHE-ALA-PHE-5T3-SER-NH2


Theoretical massNumber of molelcules
Total (without water)8,2022
Polymers8,2022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
22
V: Chromodomain Y-like protein 2
VV: IVA-PHE-ALA-PHE-5T3-SER-NH2


Theoretical massNumber of molelcules
Total (without water)8,2022
Polymers8,2022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
23
W: Chromodomain Y-like protein 2
WW: IVA-PHE-ALA-PHE-5T3-SER-NH2


Theoretical massNumber of molelcules
Total (without water)8,2022
Polymers8,2022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
24
X: Chromodomain Y-like protein 2
XX: IVA-PHE-ALA-PHE-5T3-SER-NH2


  • defined by author
  • 8.2 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)8,2023
Polymers8,2022
Non-polymers01
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
25
Y: Chromodomain Y-like protein 2
YY: IVA-PHE-ALA-PHE-5T3-SER-NH2


  • defined by author
  • 8.2 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)8,2023
Polymers8,2022
Non-polymers01
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
26
Z: Chromodomain Y-like protein 2
ZZ: IVA-PHE-ALA-PHE-5T3-SER-NH2


  • defined by author
  • 8.2 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)8,2023
Polymers8,2022
Non-polymers01
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.840, 82.160, 128.630
Angle α, β, γ (deg.)90.000, 97.440, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
131
141
151
161
171
181
191
201
211
221
231
241
251
261
12
22
32
42
52
62
72
82
92
102
112
122
132
142
152
162
172
182
192
202
212
222
232
242
252

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYILEILE(chain 'AA' and (resid 4 through 10 or (resid 11...AA4 - 524 - 52
211GLYGLYILEILE(chain 'AC' and (resid 4 through 10 or (resid 11...BC4 - 524 - 52
311GLYGLYILEILE(chain 'BA' and (resid 4 through 10 or (resid 11...CE4 - 524 - 52
411GLYGLYILEILE(chain 'BC' and (resid 4 through 10 or (resid 11...DG4 - 524 - 52
511GLYGLYILEILE(chain 'CA' and (resid 4 through 10 or (resid 11...EI4 - 524 - 52
611GLYGLYILEILE(chain 'CC' and (resid 4 through 10 or (resid 11...FK4 - 524 - 52
711GLYGLYILEILE(chain 'DA' and (resid 4 through 12 or (resid 13...GM4 - 524 - 52
811GLYGLYILEILE(chain 'DC' and (resid 4 through 10 or (resid 11...HO4 - 524 - 52
911GLYGLYILEILE(chain 'EA' and (resid 4 through 10 or (resid 11...IQ4 - 524 - 52
1011GLYGLYILEILE(chain 'EC' and (resid 4 through 10 or (resid 11...JS4 - 524 - 52
1111GLYGLYILEILE(chain 'FA' and (resid 4 through 10 or (resid 11...KU4 - 524 - 52
1211GLYGLYILEILE(chain 'FC' and (resid 4 through 10 or (resid 11...LW4 - 524 - 52
1311GLYGLYILEILE(chain 'GA' and (resid 4 through 10 or (resid 11...MY4 - 524 - 52
1411GLYGLYILEILE(chain 'GC' and (resid 4 through 10 or (resid 11...NAA4 - 524 - 52
1511GLYGLYILEILE(chain 'HA' and (resid 4 through 10 or (resid 11...OCA4 - 524 - 52
1611GLYGLYILEILE(chain 'HC' and (resid 4 through 10 or (resid 11...PEA4 - 524 - 52
1711GLYGLYILEILE(chain 'IA' and (resid 4 through 10 or (resid 11...QGA4 - 524 - 52
1811GLYGLYILEILE(chain 'IC' and (resid 4 through 10 or (resid 11...RIA4 - 524 - 52
1911GLYGLYILEILE(chain 'JA' and (resid 4 through 10 or (resid 11...SKA4 - 524 - 52
2011GLYGLYILEILE(chain 'JC' and (resid 4 through 10 or (resid 11...TMA4 - 524 - 52
2111GLYGLYILEILE(chain 'KA' and (resid 4 through 10 or (resid 11...UOA4 - 524 - 52
2211GLYGLYILEILE(chain 'KC' and (resid 4 through 10 or (resid 11...VQA4 - 524 - 52
2311GLYGLYILEILE(chain 'LA' and (resid 4 through 10 or (resid 11...WSA4 - 524 - 52
2411GLYGLYILEILE(chain 'LC' and (resid 4 through 10 or (resid 11...XUA4 - 524 - 52
2511GLYGLYILEILE(chain 'MA' and (resid 4 through 10 or (resid 11...YWA4 - 524 - 52
2611GLYGLYILEILE(chain 'MC' and (resid 4 through 10 or (resid 11...ZYA4 - 524 - 52
112PHEPHEPHEPHE(chain 'AB' and (resid 1 through 3 or (resid 4...AAB12
122PHEPHE5T35T3(chain 'AB' and (resid 1 through 3 or (resid 4...AAB3 - 44 - 5
212PHEPHEPHEPHE(chain 'AD' and (resid 1 through 3 or (resid 4...BBD12
222PHEPHE5T35T3(chain 'AD' and (resid 1 through 3 or (resid 4...BBD3 - 44 - 5
312PHEPHEPHEPHE(chain 'BB' and (resid 1 through 3 or (resid 4...CCF12
322PHEPHE5T35T3(chain 'BB' and (resid 1 through 3 or (resid 4...CCF3 - 44 - 5
412PHEPHEPHEPHE(chain 'BD' and (resid 1 through 3 or (resid 4...DDH12
422PHEPHE5T35T3(chain 'BD' and (resid 1 through 3 or (resid 4...DDH3 - 44 - 5
512PHEPHEPHEPHE(chain 'CB' and (resid 1 through 3 or (resid 4...EEJ12
522PHEPHE5T35T3(chain 'CB' and (resid 1 through 3 or (resid 4...EEJ3 - 44 - 5
612PHEPHEPHEPHE(chain 'CD' and (resid 1 through 3 or (resid 4...FFL12
622PHEPHE5T35T3(chain 'CD' and (resid 1 through 3 or (resid 4...FFL3 - 44 - 5
712PHEPHEPHEPHE(chain 'DB' and (resid 1 through 3 or (resid 4...GGN12
722PHEPHE5T35T3(chain 'DB' and (resid 1 through 3 or (resid 4...GGN3 - 44 - 5
812PHEPHEPHEPHE(chain 'DD' and (resid 1 through 3 or (resid 4...HHP12
822PHEPHE5T35T3(chain 'DD' and (resid 1 through 3 or (resid 4...HHP3 - 44 - 5
912PHEPHEPHEPHE(chain 'EB' and (resid 1 through 3 or (resid 4...IIR12
922PHEPHE5T35T3(chain 'EB' and (resid 1 through 3 or (resid 4...IIR3 - 44 - 5
1012PHEPHEPHEPHE(chain 'ED' and (resid 1 through 3 or (resid 4...JJT12
1022PHEPHE5T35T3(chain 'ED' and (resid 1 through 3 or (resid 4...JJT3 - 44 - 5
1112PHEPHEPHEPHE(chain 'FB' and (resid 1 through 3 or (resid 4...KKV12
1122PHEPHE5T35T3(chain 'FB' and (resid 1 through 3 or (resid 4...KKV3 - 44 - 5
1212PHEPHEPHEPHE(chain 'FD' and (resid 1 through 3 or (resid 4...LLX12
1222PHEPHE5T35T3(chain 'FD' and (resid 1 through 3 or (resid 4...LLX3 - 44 - 5
1312PHEPHEPHEPHE(chain 'GB' and (resid 1 through 3 or (resid 4...MMZ12
1322PHEPHE5T35T3(chain 'GB' and (resid 1 through 3 or (resid 4...MMZ3 - 44 - 5
1412PHEPHEPHEPHE(chain 'GD' and (resid 1 through 3 or (resid 4...NNBA12
1422PHEPHE5T35T3(chain 'GD' and (resid 1 through 3 or (resid 4...NNBA3 - 44 - 5
1512PHEPHEPHEPHE(chain 'HB' and (resid 1 through 3 or (resid 4...OODA12
1522PHEPHE5T35T3(chain 'HB' and (resid 1 through 3 or (resid 4...OODA3 - 44 - 5
1612PHEPHEPHEPHE(chain 'HD' and (resid 1 through 4 or (resid 5 and (name N or name CA ))))PPFA12
1622PHEPHE5T35T3(chain 'HD' and (resid 1 through 4 or (resid 5 and (name N or name CA ))))PPFA3 - 44 - 5
1712PHEPHEPHEPHE(chain 'IB' and (resid 1 through 3 or (resid 4...QQHA12
1722PHEPHE5T35T3(chain 'IB' and (resid 1 through 3 or (resid 4...QQHA3 - 44 - 5
1812PHEPHEPHEPHE(chain 'ID' and (resid 1 through 3 or (resid 4...RRJA12
1822PHEPHE5T35T3(chain 'ID' and (resid 1 through 3 or (resid 4...RRJA3 - 44 - 5
1912PHEPHEPHEPHE(chain 'JB' and (resid 1 through 3 or (resid 4...SSLA12
1922PHEPHE5T35T3(chain 'JB' and (resid 1 through 3 or (resid 4...SSLA3 - 44 - 5
2012PHEPHEPHEPHE(chain 'JD' and (resid 1 through 3 or (resid 4...TTNA12
2022PHEPHE5T35T3(chain 'JD' and (resid 1 through 3 or (resid 4...TTNA3 - 44 - 5
2112PHEPHEPHEPHE(chain 'KD' and (resid 1 through 3 or (resid 4...VVRA12
2122PHEPHE5T35T3(chain 'KD' and (resid 1 through 3 or (resid 4...VVRA3 - 44 - 5
2212PHEPHEPHEPHE(chain 'LB' and (resid 1 through 3 or (resid 4...WWTA12
2222PHEPHE5T35T3(chain 'LB' and (resid 1 through 3 or (resid 4...WWTA3 - 44 - 5
2312PHEPHEPHEPHE(chain 'LD' and (resid 1 through 3 or (resid 4...XXVA12
2322PHEPHE5T35T3(chain 'LD' and (resid 1 through 3 or (resid 4...XXVA3 - 44 - 5
2412PHEPHEPHEPHE(chain 'MB' and (resid 1 through 3 or (resid 4...YYXA12
2422PHEPHE5T35T3(chain 'MB' and (resid 1 through 3 or (resid 4...YYXA3 - 44 - 5
2512PHEPHEPHEPHE(chain 'MD' and (resid 1 through 3 or (resid 4...ZZZA12
2522PHEPHE5T35T3(chain 'MD' and (resid 1 through 3 or (resid 4...ZZZA3 - 44 - 5

NCS ensembles :
ID
1
2

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Components

#1: Protein ...
Chromodomain Y-like protein 2 / CDY-like 2


Mass: 7451.329 Da / Num. of mol.: 26 / Fragment: chromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDYL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8N8U2
#2: Protein/peptide ...
IVA-PHE-ALA-PHE-5T3-SER-NH2


Mass: 750.948 Da / Num. of mol.: 26 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 28 / Source method: obtained synthetically
Has ligand of interestY

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Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 15% PEG8000, 0.2 M MgCl2 and 0.1 M Tris-HCl pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97901 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionResolution: 2.7→36.25 Å / Num. obs: 50439 / % possible obs: 99.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 42.26 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.129 / Rrim(I) all: 0.15 / Net I/σ(I): 9
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allNet I/σ(I) obs
12.08-36.2594.73.40.0395740.9970.04625
2.7-2.7798.63.70.87536600.5411.0221.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: from early version of PDB entry 6v2d

6v2d


Resolution: 2.8→36.25 Å / SU ML: 0.4002 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.6138
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2705 2234 4.93 %
Rwork0.2045 43083 -
obs0.2077 45317 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.68 Å2
Refinement stepCycle: LAST / Resolution: 2.8→36.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12223 0 28 0 12251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812587
X-RAY DIFFRACTIONf_angle_d1.029217017
X-RAY DIFFRACTIONf_chiral_restr0.05891661
X-RAY DIFFRACTIONf_plane_restr0.00582301
X-RAY DIFFRACTIONf_dihedral_angle_d27.31274597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.860.32221340.23942651X-RAY DIFFRACTION99.36
2.86-2.930.3521530.25432664X-RAY DIFFRACTION99.54
2.93-30.34461350.26072663X-RAY DIFFRACTION99.54
3-3.080.35641530.24972659X-RAY DIFFRACTION99.54
3.08-3.170.2971340.23922718X-RAY DIFFRACTION99.65
3.17-3.270.32521410.22162664X-RAY DIFFRACTION99.5
3.27-3.390.27721450.21072652X-RAY DIFFRACTION99.68
3.39-3.530.25281280.20022702X-RAY DIFFRACTION99.61
3.53-3.690.26371500.20172689X-RAY DIFFRACTION99.54
3.69-3.880.26641370.18572685X-RAY DIFFRACTION99.68
3.88-4.120.21081390.1712689X-RAY DIFFRACTION99.86
4.12-4.440.26191290.1642725X-RAY DIFFRACTION99.69
4.44-4.890.24681270.15022723X-RAY DIFFRACTION99.82
4.89-5.590.20341320.18032720X-RAY DIFFRACTION99.72
5.59-7.040.24031380.22262723X-RAY DIFFRACTION99.76
7.04-36.250.29871590.26412756X-RAY DIFFRACTION98.75

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