Macromolecules
Sequence Display for 4IXQ

Classification: PHOTOSYNTHESIS

Total Structure Weight: 765686.00

Macromolecule Entities
Molecule Chains Length Organism Details
Photosystem Q(B) protein 1 A, a 360 Thermosynechococcus elongatus EC#: 1.10.3.9 IUBMB
Gene Name(s): psbA1 psbA-1 tlr1843
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II core light harvesting protein B, b 510 Thermosynechococcus elongatus Gene Name(s): psbB tlr1530
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II CP43 protein C, c 461 Thermosynechococcus elongatus Gene Name(s): psbC tlr1631
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II D2 protein D, d 352 Thermosynechococcus elongatus EC#: 1.10.3.9 IUBMB
Gene Name(s): psbD1 tlr0455 psbD2 tlr1630
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome b559 subunit alpha E, e 84 Thermosynechococcus elongatus Gene Name(s): psbE tsr1541
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome b559 subunit beta F, f 45 Thermosynechococcus elongatus Gene Name(s): psbF tsr1542
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center protein H H, h 66 Thermosynechococcus elongatus Gene Name(s): psbH tsl1386
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center protein I I, i 38 Thermosynechococcus elongatus Gene Name(s): psbI tsr1074
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center protein J J, j 40 Thermosynechococcus elongatus Gene Name(s): psbJ tsr1544
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center protein K K, k 46 Thermosynechococcus elongatus Gene Name(s): psbK tsl0176
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center protein L L, l 37 Thermosynechococcus elongatus Gene Name(s): psbL tsr1543
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center protein M M, m 36 Thermosynechococcus elongatus Gene Name(s): psbM tsl2052
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II manganese-stabilizing polypeptide O, o 272 Thermosynechococcus elongatus Gene Name(s): psbO tll0444
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center protein T T, t 32 Thermosynechococcus elongatus Gene Name(s): psbT tsr1531
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II 12 kDa extrinsic protein U, u 134 Thermosynechococcus elongatus Gene Name(s): psbU tll2409
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome c-550 V, v 163 Thermosynechococcus elongatus Gene Name(s): psbV tll1285
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center protein ycf12 g, y 46 Thermosynechococcus elongatus Gene Name(s): ycf12 tsr1242
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center X protein X, x 41 Thermosynechococcus elongatus Gene Name(s): psbX tsr2013
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center protein Z Z, z 62 Thermosynechococcus elongatus Gene Name(s): psbZ tsr1967
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center protein Y G, Y 28 Thermosynechococcus elongatus Fragment: SEE REMARK 999

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

Subgroup Name: Photosystems

Protein Name: Photosystem II


Small Molecules
Ligands 15 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DGD
Query on DGD

A, B, C, D, a, b, c, d DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CLA
Query on CLA

A, B, C, D, a, b, c, d CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PHO
Query on PHO

A, D, a PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SQD
Query on SQD

A, B, D, F, a, b, d, f 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA- D-GLUCOPYRANOSYL]-SN-GLYCEROL
SULFOQUINOVOSYLDIACYLGLYCEROL (Synonym)
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LMG
Query on LMG

A, B, C, D, E, I, M, a, b, c, d, e, i, k 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PL9
Query on PL9

A, D, J, a, d, j 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
PLASTOQUINONE 9 (Synonym)
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LHG
Query on LHG

A, a 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEM
Query on HEM

F, V, f, v PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BCR
Query on BCR

A, B, C, D, H, J, K, T, Z, a, b, c, f, j, k, x BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LMT
Query on LMT

B, D, I, M, T, b, i, m, x DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OEC
Query on OEC

A, a OXYGEN EVOLVING SYSTEM
Ca Mn4 O4
UFRGXNUNWYSFQE-MBOUAFFSAW
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BCT
Query on BCT

A, d BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE2
Query on FE2

A, a FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

K, O, k, o CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, d CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
UNK
Query on UNK
G, Y L-PEPTIDE LINKING C4 H9 N O2 --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.7 Å
  • R-Value Free: 0.314
  • R-Value Work: 0.277
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 131.86 α = 90.00
b = 227.51 β = 90.00
c = 307.22 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-01-27
  • Released Date: 2013-02-20
  • Deposition author(s): Kern, J., Alonso-Mori, R., Tran, R., Hattne, J., Gildea, R.J., Echols, N., Gloeckner, C., Hellmich, J., Laksmono, H., Sierra, R.G., Lassalle-Kaiser, B., Koroidov, S., Lampe, A., Han, G., Gul, S., DiFiore, D., Milathianaki, D., Fry, A.R., Miahnahri, A., Schafer, D.W., Messerschmidt, M., Seibert, M.M., Koglin, J.E., Sokaras, D., Weng, T.-C., Sellberg, J., Latimer, M.J., Grosse-Kunstleve, R.W., Zwart, P.H., White, W.E., Glatzel, P., Adams, P.D., Bogan, M.J., Williams, G.J., Boutet, S., Messinger, J., Zouni, A., Sauter, N.K., Yachandra, V.K., Bergmann, U., Yano, J.

Revision History

  • Version 1_0: 2013-02-20

    Type: Initial release

  • Version 1_1: 2013-02-27

    Type: Database references

  • Version 1_2: 2013-05-08

    Type: Database references