8GN0 | pdb_00008gn0

Crystal structure of DCBQ-bound photosystem II complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.185 (Depositor), 0.185 (DCC) 
  • R-Value Work: 
    0.151 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 
    0.153 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history

Literature

Structural insights into the action mechanisms of artificial electron acceptors in photosystem II.

Kamada, S.Nakajima, Y.Shen, J.R.

(2023) J Biological Chem 299: 104839-104839

  • DOI: https://doi.org/10.1016/j.jbc.2023.104839
  • Primary Citation Related Structures: 
    8GN0, 8GN1, 8GN2

  • PubMed Abstract: 

    Photosystem II (PSII) utilizes light energy to split water, and the electrons extracted from water are transferred to Q B , a plastoquinone molecule bound to the D1 subunit of PSII. Many artificial electron acceptors (AEAs) with molecular structures similar to that of plastoquinone can accept electrons from PSII. However, the molecular mechanism by which AEAs act on PSII is unclear. Here, we solved the crystal structure of PSII treated with three different AEAs, 2,5-dibromo-1,4-benzoquinone, 2,6-dichloro-1,4-benzoquinone, and 2-phenyl-1,4-benzoquinone, at 1.95 to 2.10 Å resolution. Our results show that all AEAs substitute for Q B and are bound to the Q B -binding site (Q B site) to receive electrons, but their binding strengths are different, resulting in differences in their efficiencies to accept electrons. The acceptor 2-phenyl-1,4-benzoquinone binds most weakly to the Q B site and showed the highest oxygen-evolving activity, implying a reverse relationship between the binding strength and oxygen-evolving activity. In addition, a novel quinone-binding site, designated the Q D site, was discovered, which is located in the vicinity of Q B site and close to Q C site, a binding site reported previously. This Q D site is expected to play a role as a channel or a storage site for quinones to be transported to the Q B site. These results provide the structural basis for elucidating the actions of AEAs and exchange mechanism of Q B in PSII and also provide information for the design of more efficient electron acceptors.


  • Organizational Affiliation
    • Faculty of Science, Okayama University, Okayama, Japan.

Macromolecule Content 

  • Total Structure Weight: 747.39 kDa 
  • Atom Count: 53,814 
  • Modeled Residue Count: 5,220 
  • Deposited Residue Count: 5,346 
  • Unique protein chains: 19

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein D1A,
T [auth a]
344Thermostichus vulcanusMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
U [auth b]
505Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
V [auth c]
455Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
W [auth d]
342Thermostichus vulcanusMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
X [auth e]
83Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Y [auth f]
44Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HG [auth H],
Z [auth h]
63Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IAA [auth i],
H [auth I]
38Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JBA [auth j],
I [auth J]
40Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KCA [auth k],
J [auth K]
37Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LDA [auth l],
K [auth L]
37Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MEA [auth m],
L [auth M]
36Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideFA [auth o],
M [auth O]
244Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TGA [auth t],
N [auth T]
32Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinHA [auth u],
O [auth U]
104Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c-550IA [auth v],
P [auth V]
137Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12JA [auth y],
Q [auth Y]
30Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein XKA [auth x],
R [auth X]
40Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZLA [auth z],
S [auth Z]
62Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence

Small Molecules

Ligands 23 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD



Download:Ideal Coordinates CCD File
CE [auth C]
DE [auth C]
DF [auth D]
EE [auth C]
NL [auth c]
CE [auth C],
DE [auth C],
DF [auth D],
EE [auth C],
NL [auth c],
OL [auth c],
PL [auth c],
VN [auth h],
ZF [auth H]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA

Query on CLA



Download:Ideal Coordinates CCD File
AC [auth B]
AF [auth D]
AL [auth c]
AN [auth d]
BC [auth B]
AC [auth B],
AF [auth D],
AL [auth c],
AN [auth d],
BC [auth B],
BL [auth c],
BN [auth d],
CC [auth B],
CL [auth c],
DC [auth B],
DL [auth c],
EC [auth B],
EL [auth c],
FC [auth B],
FL [auth c],
GC [auth B],
GL [auth c],
HL [auth c],
IL [auth c],
JJ [auth b],
JL [auth c],
KJ [auth b],
KL [auth c],
LJ [auth b],
LL [auth c],
MJ [auth b],
ND [auth C],
NJ [auth b],
OD [auth C],
OI [auth a],
OJ [auth b],
PD [auth C],
PI [auth a],
PJ [auth b],
QA [auth A],
QD [auth C],
QJ [auth b],
RA [auth A],
RB [auth B],
RD [auth C],
RJ [auth b],
SA [auth A],
SB [auth B],
SD [auth C],
SI [auth a],
SJ [auth b],
TB [auth B],
TD [auth C],
TJ [auth b],
UB [auth B],
UD [auth C],
UJ [auth b],
UM [auth d],
VA [auth A],
VB [auth B],
VD [auth C],
VJ [auth b],
WB [auth B],
WD [auth C],
WJ [auth b],
XB [auth B],
XD [auth C],
XJ [auth b],
YB [auth B],
YD [auth C],
YJ [auth b],
ZB [auth B],
ZD [auth C],
ZE [auth D],
ZK [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO

Query on PHO



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QI [auth a],
RI [auth a],
TA [auth A],
UA [auth A]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD

Query on SQD



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EF [auth D]
EJ [auth b]
FO [auth l]
II [auth a]
JN [auth d]
EF [auth D],
EJ [auth b],
FO [auth l],
II [auth a],
JN [auth d],
KC [auth B],
UI [auth a],
XA [auth A],
YE [auth D]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG

Query on LMG



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FE [auth C]
GN [auth d]
IF [auth D]
KO [auth m]
LC [auth B]
FE [auth C],
GN [auth d],
IF [auth D],
KO [auth m],
LC [auth B],
ME [auth C],
QL [auth c],
RL [auth c],
WK [auth c],
YA [auth A]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
(Subject of Investigation/LOI)

Query on PL9



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CF [auth D],
DN [auth d],
HB [auth A],
YP [auth x]
2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
LHG

Query on LHG



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EN [auth d]
FF [auth D]
FN [auth d]
GF [auth D]
HF [auth D]
EN [auth d],
FF [auth D],
FN [auth d],
GF [auth D],
HF [auth D],
HO [auth l],
JG [auth L],
QN [auth e],
RF [auth E],
VM [auth d]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEC

Query on HEC



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JP [auth v],
PH [auth V]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM

Query on HEM



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SN [auth e],
VF [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
RRX

Query on RRX



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UN [auth h],
YF [auth H]
(3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
BCR

Query on BCR



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AE [auth C]
AK [auth b]
AQ [auth z]
BE [auth C]
BF [auth D]
AE [auth C],
AK [auth b],
AQ [auth z],
BE [auth C],
BF [auth D],
BK [auth b],
CN [auth d],
DI [auth Y],
DO [auth k],
GH [auth T],
HC [auth B],
HG [auth K],
IC [auth B],
JC [auth B],
ML [auth c],
TI [auth a],
WA [auth A],
WC [auth B],
XP [auth y],
ZJ [auth b]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT

Query on LMT



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BQ [auth z]
FB [auth A]
FG [auth J]
FI [auth Z]
HH [auth T]
BQ [auth z],
FB [auth A],
FG [auth J],
FI [auth Z],
HH [auth T],
KG [auth M],
LG [auth M],
LO [auth m],
MC [auth B],
MO [auth m],
TM [auth d],
TN [auth f],
WF [auth F],
WM [auth d],
XC [auth B],
YN [auth i],
ZA [auth A],
ZN [auth j]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX

Query on OEX



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JI [auth a],
MA [auth A]
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
HTG

Query on HTG



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BG [auth I]
CK [auth b]
DK [auth b]
FJ [auth b]
GE [auth C]
BG [auth I],
CK [auth b],
DK [auth b],
FJ [auth b],
GE [auth C],
GJ [auth b],
HE [auth C],
HJ [auth b],
HN [auth d],
KE [auth C],
NC [auth B],
NO [auth o],
OC [auth B],
PC [auth B],
QC [auth B],
SH [auth V],
SL [auth c],
TL [auth c],
VL [auth c],
XF [auth H],
XN [auth i],
ZM [auth d]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
JOX
(Subject of Investigation/LOI)

Query on JOX



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DB [auth A],
EB [auth A],
WI [auth a],
YI [auth a]
2,6-bis(chloranyl)cyclohexa-2,5-diene-1,4-dione
C6 H2 Cl2 O2
JCARTGJGWCGSSU-UHFFFAOYSA-N
GOL

Query on GOL



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AB [auth A]
AM [auth c]
CB [auth A]
DG [auth J]
FP [auth u]
AB [auth A],
AM [auth c],
CB [auth A],
DG [auth J],
FP [auth u],
HI [auth a],
IK [auth b],
IN [auth d],
JE [auth C],
KH [auth U],
KP [auth v],
LD [auth B],
LE [auth C],
LH [auth U],
LP [auth v],
MP [auth v],
NG [auth O],
OG [auth O],
PG [auth O],
PO [auth o],
QG [auth O],
RH [auth V],
TC [auth B],
UF [auth E],
VC [auth B],
VK [auth b],
XE [auth D],
XI [auth a],
YL [auth c],
ZL [auth c]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
AD [auth B]
AG [auth H]
AH [auth O]
AI [auth V]
AJ [auth a]
AD [auth B],
AG [auth H],
AH [auth O],
AI [auth V],
AJ [auth a],
AP [auth o],
BD [auth B],
BH [auth O],
BI [auth V],
BJ [auth a],
BM [auth c],
BP [auth o],
CD [auth B],
CH [auth O],
CJ [auth a],
CM [auth c],
CP [auth o],
DD [auth B],
DH [auth O],
DJ [auth a],
DM [auth c],
ED [auth B],
EH [auth O],
EI [auth X],
EM [auth c],
EP [auth t],
FD [auth B],
FM [auth c],
GD [auth B],
GM [auth c],
GP [auth u],
HD [auth B],
HM [auth c],
HP [auth u],
ID [auth B],
IH [auth T],
IM [auth c],
IO [auth l],
IP [auth u],
JB [auth A],
JD [auth B],
JH [auth T],
JM [auth c],
KB [auth A],
KD [auth B],
KK [auth b],
KM [auth c],
KN [auth d],
LB [auth A],
LK [auth b],
LM [auth c],
LN [auth d],
MB [auth A],
MF [auth D],
MH [auth U],
MK [auth b],
MM [auth c],
MN [auth d],
NB [auth A],
NE [auth C],
NF [auth D],
NH [auth U],
NK [auth b],
NM [auth c],
NN [auth d],
NP [auth v],
OB [auth A],
OE [auth C],
OF [auth D],
OH [auth U],
OK [auth b],
OM [auth c],
ON [auth d],
OP [auth v],
PB [auth A],
PE [auth C],
PF [auth D],
PK [auth b],
PM [auth c],
PN [auth d],
PP [auth v],
QE [auth C],
QF [auth D],
QH [auth V],
QK [auth b],
QM [auth c],
QO [auth o],
QP [auth v],
RE [auth C],
RG [auth O],
RK [auth b],
RM [auth c],
RO [auth o],
RP [auth v],
SE [auth C],
SG [auth O],
SK [auth b],
SM [auth c],
SO [auth o],
SP [auth v],
TE [auth C],
TG [auth O],
TH [auth V],
TK [auth b],
TO [auth o],
TP [auth v],
UE [auth C],
UG [auth O],
UH [auth V],
UK [auth b],
UO [auth o],
UP [auth v],
VE [auth C],
VG [auth O],
VH [auth V],
VO [auth o],
VP [auth v],
WE [auth C],
WG [auth O],
WH [auth V],
WO [auth o],
WP [auth v],
XG [auth O],
XH [auth V],
XO [auth o],
YC [auth B],
YG [auth O],
YH [auth V],
YO [auth o],
ZC [auth B],
ZG [auth O],
ZH [auth V],
ZI [auth a],
ZO [auth o]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
BCT

Query on BCT



Download:Ideal Coordinates CCD File
GB [auth A],
NI [auth a]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2

Query on FE2



Download:Ideal Coordinates CCD File
KI [auth a],
NA [auth A]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
IJ [auth b],
MG [auth O],
OO [auth o],
QB [auth B],
YK [auth c]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
LI [auth a],
MI [auth a],
OA [auth A],
PA [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
BO [auth j],
EG [auth J],
EO [auth k],
IG [auth K]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL

Query on UNL



Download:Ideal Coordinates CCD File
AO [auth j]
BB [auth A]
CG [auth I]
CI [auth Y]
CO [auth k]
AO [auth j],
BB [auth A],
CG [auth I],
CI [auth Y],
CO [auth k],
DP [auth t],
EK [auth b],
FH [auth T],
FK [auth b],
GG [auth J],
GI [auth a],
GK [auth b],
GO [auth l],
HK [auth b],
IB [auth A],
IE [auth C],
JF [auth D],
JK [auth b],
JO [auth m],
KF [auth D],
LF [auth D],
MD [auth C],
RC [auth B],
RN [auth e],
SC [auth B],
SF [auth E],
TF [auth E],
UC [auth B],
UL [auth c],
VI [auth a],
WL [auth c],
WN [auth i],
XK [auth c],
XL [auth c],
XM [auth d],
YM [auth d],
ZP [auth x]
Unknown ligand
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
HSK
Query on HSK
D,
W [auth d]
L-PEPTIDE LINKINGC6 H9 N3 O3HIS
FME
Query on FME
AA [auth i],
H [auth I]
L-PEPTIDE LINKINGC6 H11 N O3 SMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.185 (Depositor), 0.185 (DCC) 
  • R-Value Work:  0.151 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 0.153 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.223α = 90
b = 228.205β = 90
c = 286.997γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-05
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Derived calculations, Refinement description
  • Version 2.0: 2025-07-30
    Changes: Atomic model, Data collection, Derived calculations, Structure summary