5ZZN | pdb_00005zzn

Crystal structure of photosystem II from an SQDG-deficient mutant of Thermosynechococcus elongatus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.197 (Depositor), 0.202 (DCC) 
  • R-Value Work: 
    0.154 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 
    0.156 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 4.0 of the entry. See complete history

Literature

Thylakoid membrane lipid sulfoquinovosyl-diacylglycerol (SQDG) is required for full functioning of photosystem II inThermosynechococcus elongatus.

Nakajima, Y.Umena, Y.Nagao, R.Endo, K.Kobayashi, K.Akita, F.Suga, M.Wada, H.Noguchi, T.Shen, J.R.

(2018) J Biological Chem 293: 14786-14797

  • DOI: https://doi.org/10.1074/jbc.RA118.004304
  • Primary Citation Related Structures: 
    5ZZN

  • PubMed Abstract: 

    Sulfoquinovosyl-diacylglycerol (SQDG) is one of the four lipids present in the thylakoid membranes. Depletion of SQDG causes different degrees of effects on photosynthetic growth and activities in different organisms. Four SQDG molecules bind to each monomer of photosystem II (PSII), but their role in PSII function has not been characterized in detail, and no PSII structure without SQDG has been reported. We analyzed the activities of PSII from an SQDG-deficient mutant of the cyanobacterium Thermosynechococcus elongatus by various spectroscopic methods, which showed that depletion of SQDG partially impaired the PSII activity by impairing secondary quinone (Q B ) exchange at the acceptor site. We further solved the crystal structure of the PSII dimer from the SQDG deletion mutant at 2.1 Å resolution and found that all of the four SQDG-binding sites were occupied by other lipids, most likely PG molecules. Replacement of SQDG at a site near the head of Q B provides a possible explanation for the Q B impairment. The replacement of two SQDGs located at the monomer-monomer interface by other lipids decreased the stability of the PSII dimer, resulting in an increase in the amount of PSII monomer in the mutant. The present results thus suggest that although SQDG binding in all of the PSII-binding sites is necessary to fully maintain the activity and stability of PSII, replacement of SQDG by other lipids can partially compensate for their functions.


  • Organizational Affiliation
    • From the Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530.

Macromolecule Content 

  • Total Structure Weight: 756.99 kDa 
  • Atom Count: 53,800 
  • Modeled Residue Count: 5,254 
  • Deposited Residue Count: 5,270 
  • Unique protein chains: 19

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein D1 1A,
T [auth a]
334Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for P0A444 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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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]
505Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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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]
455Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
W [auth d]
342Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
X [auth e]
81Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Y [auth f]
34Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DIN9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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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]
63Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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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]
37Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DJZ6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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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]
40Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P59087 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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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]
37Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9F1K9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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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]
36Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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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]
34Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DHA7 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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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]
243Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TGA [auth t],
N [auth T]
30Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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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]
97Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9F1L5 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c-550IA [auth v],
P [auth V]
137Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A386 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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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]
29Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinKA [auth x],
R [auth X]
39Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9F1R6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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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]
62Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DHJ2 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence

Small Molecules

Ligands 21 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD



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DM [auth h]
GK [auth c]
HK [auth c]
IK [auth c]
JF [auth H]
DM [auth h],
GK [auth c],
HK [auth c],
IK [auth c],
JF [auth H],
MD [auth C],
ML [auth d],
ND [auth C],
OD [auth C],
PE [auth D]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA

Query on CLA



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AD [auth C]
AK [auth c]
BD [auth C]
BK [auth c]
CD [auth C]
AD [auth C],
AK [auth c],
BD [auth C],
BK [auth c],
CD [auth C],
CK [auth c],
DD [auth C],
DK [auth c],
ED [auth C],
FD [auth C],
FI [auth b],
GD [auth C],
GI [auth b],
GL [auth d],
HD [auth C],
HI [auth b],
HL [auth d],
IB [auth B],
ID [auth C],
II [auth b],
JB [auth B],
JD [auth C],
JI [auth b],
JL [auth d],
KB [auth B],
KD [auth C],
KE [auth D],
KI [auth b],
LB [auth B],
LH [auth a],
LI [auth b],
MB [auth B],
ME [auth D],
MH [auth a],
MI [auth b],
NB [auth B],
NI [auth b],
OB [auth B],
OH [auth a],
OI [auth b],
PA [auth A],
PB [auth B],
PI [auth b],
QA [auth A],
QB [auth B],
QI [auth b],
RA [auth A],
RB [auth B],
RI [auth b],
RJ [auth c],
SB [auth B],
SI [auth b],
SJ [auth c],
TA [auth A],
TB [auth B],
TI [auth b],
TJ [auth c],
UB [auth B],
UI [auth b],
UJ [auth c],
VB [auth B],
VJ [auth c],
WB [auth B],
WJ [auth c],
XB [auth B],
XJ [auth c],
YC [auth C],
YJ [auth c],
ZC [auth C],
ZJ [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO

Query on PHO



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IL [auth d],
LE [auth D],
NH [auth a],
SA [auth A]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
LMG

Query on LMG



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CC [auth B]
JK [auth c]
KK [auth c]
PD [auth C]
QD [auth C]
CC [auth B],
JK [auth c],
KK [auth c],
PD [auth C],
QD [auth C],
QL [auth d],
RH [auth a],
TE [auth D],
WA [auth A],
ZI [auth b]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9

Query on PL9



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LL [auth d],
OE [auth D],
QH [auth a],
VA [auth A]
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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BC [auth B]
CF [auth E]
CM [auth f]
IF [auth F]
NL [auth d]
BC [auth B],
CF [auth E],
CM [auth f],
IF [auth F],
NL [auth d],
OL [auth d],
PL [auth d],
QE [auth D],
RE [auth D],
SE [auth D],
WL [auth e],
YI [auth b]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEC

Query on HEC



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

Query on HEM



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BM [auth f],
GF [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
RRX

Query on RRX



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

Query on BCR



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AC [auth B]
CH [auth Y]
EK [auth c]
FK [auth c]
GN [auth t]
AC [auth B],
CH [auth Y],
EK [auth c],
FK [auth c],
GN [auth t],
KL [auth d],
LD [auth C],
NE [auth D],
NG [auth T],
PH [auth a],
PM [auth k],
UA [auth A],
VF [auth K],
VI [auth b],
WF [auth K],
WI [auth b],
WN [auth y],
XI [auth b],
YB [auth B],
ZB [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT

Query on LMT



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AB [auth A]
AG [auth M]
AJ [auth b]
DC [auth B]
EH [auth Z]
AB [auth A],
AG [auth M],
AJ [auth b],
DC [auth B],
EH [auth Z],
GH [auth a],
HF [auth F],
HN [auth t],
LK [auth c],
MM [auth j],
OG [auth T],
RD [auth C],
RM [auth l],
SM [auth m],
TF [auth J],
TM [auth m],
UM [auth m],
YN [auth z],
ZF [auth M]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX

Query on OEX



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

Query on HTG



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BI [auth b]
BJ [auth b]
CG [auth O]
CI [auth b]
EC [auth B]
BI [auth b],
BJ [auth b],
CG [auth O],
CI [auth b],
EC [auth B],
EL [auth c],
GE [auth C],
HE [auth C],
IC [auth B],
JC [auth B],
MK [auth c],
NK [auth c],
OJ [auth b],
RL [auth d],
SD [auth C],
SG [auth U],
TD [auth C],
UE [auth D],
UG [auth V],
UN [auth v],
VM [auth o],
WC [auth B]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
GOL

Query on GOL



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EE [auth C],
KJ [auth b],
WK [auth c],
YE [auth D],
ZL [auth e]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS

Query on DMS



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AE [auth C]
AF [auth D]
AH [auth V]
AL [auth c]
AM [auth e]
AE [auth C],
AF [auth D],
AH [auth V],
AL [auth c],
AM [auth e],
AN [auth o],
BB [auth A],
BE [auth C],
BF [auth D],
BL [auth c],
BN [auth o],
CB [auth A],
CE [auth C],
CL [auth c],
CN [auth o],
DB [auth A],
DE [auth C],
DG [auth O],
DL [auth c],
DN [auth o],
EB [auth A],
EG [auth O],
EJ [auth b],
EN [auth o],
FE [auth C],
FF [auth E],
FG [auth O],
FJ [auth b],
FN [auth o],
GG [auth O],
GJ [auth b],
GM [auth h],
HG [auth O],
HJ [auth b],
IG [auth O],
IJ [auth b],
JG [auth O],
JJ [auth b],
KG [auth O],
KN [auth u],
LC [auth B],
LG [auth O],
LJ [auth b],
LN [auth u],
MC [auth B],
MG [auth O],
MJ [auth b],
MN [auth u],
NC [auth B],
NJ [auth b],
OC [auth B],
PC [auth B],
PN [auth v],
QC [auth B],
QN [auth v],
RC [auth B],
RF [auth I],
RG [auth U],
RK [auth c],
RN [auth v],
SC [auth B],
SK [auth c],
SN [auth v],
TC [auth B],
TK [auth c],
TL [auth d],
TN [auth v],
UC [auth B],
UK [auth c],
UL [auth d],
VC [auth B],
VG [auth V],
VH [auth a],
VK [auth c],
WD [auth C],
WE [auth D],
WG [auth V],
WH [auth a],
XD [auth C],
XE [auth D],
XG [auth V],
XH [auth a],
XK [auth c],
XM [auth o],
YD [auth C],
YG [auth V],
YH [auth a],
YK [auth c],
YM [auth o],
ZD [auth C],
ZE [auth D],
ZG [auth V],
ZH [auth a],
ZK [auth c],
ZM [auth o]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
BCT

Query on BCT



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FL [auth d],
JE [auth D]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2

Query on FE2



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IE [auth D],
IH [auth a]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA

Query on CA



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BG [auth O]
BH [auth V]
EI [auth b]
HB [auth B]
QJ [auth c]
BG [auth O],
BH [auth V],
EI [auth b],
HB [auth B],
QJ [auth c],
VN [auth v],
WM [auth o]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
JH [auth a],
KH [auth a],
NA [auth A],
NN [auth v],
OA [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
LM [auth j],
QM [auth k],
SF [auth J],
YF [auth K]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL

Query on UNL



Download:Ideal Coordinates CCD File
AI [auth a]
CJ [auth b]
DF [auth E]
DH [auth X]
DI [auth b]
AI [auth a],
CJ [auth b],
DF [auth E],
DH [auth X],
DI [auth b],
DJ [auth b],
EF [auth E],
FB [auth A],
FC [auth B],
FH [auth Z],
FM [auth h],
GB [auth A],
GC [auth B],
HC [auth B],
HM [auth i],
IM [auth i],
IN [auth t],
JM [auth i],
JN [auth u],
KC [auth B],
KM [auth i],
LF [auth H],
MF [auth H],
NF [auth I],
NM [auth j],
OF [auth I],
OK [auth c],
OM [auth j],
PF [auth I],
PG [auth T],
PJ [auth b],
PK [auth c],
QF [auth I],
QG [auth U],
QK [auth c],
SH [auth a],
SL [auth d],
TH [auth a],
UD [auth C],
UF [auth J],
UH [auth a],
VD [auth C],
VE [auth D],
VL [auth d],
XA [auth A],
XC [auth B],
XF [auth K],
XL [auth e],
XN [auth x],
YA [auth A],
YL [auth e],
ZA [auth A]
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: 2.10 Å
  • R-Value Free:  0.197 (Depositor), 0.202 (DCC) 
  • R-Value Work:  0.154 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 0.156 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.25α = 90
b = 228.43β = 90
c = 287.12γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building
PDB_EXTRACTdata extraction
MOLREPphasing
XDSdata reduction

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 ScienceJapanJP17H06434
Japan Society for the Promotion of ScienceJapanJP16K21181
Japan Science and TechnologyJapanJPMJPR16P1

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2018-09-05
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-03
    Changes: Data collection, Database references
  • Version 2.0: 2019-10-02
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary
  • Version 3.0: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary
  • Version 4.0: 2025-07-30
    Changes: Atomic model, Data collection, Derived calculations, Structure summary