Macromolecules
Sequence Display for 4FBY

Classification: PHOTOSYNTHESIS

Total Structure Weight: 741329.81

Macromolecule Entities
Molecule Chains Length Organism Details
Photosystem Q(B) protein 1 A, G 344 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, N 510 Thermosynechococcus elongatus Gene Name(s): psbB tlr1530
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II CP43 protein C, P 461 Thermosynechococcus elongatus Gene Name(s): psbC tlr1631
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II D2 protein D, Q 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, R 83 Thermosynechococcus elongatus Gene Name(s): psbE tsr1541
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome b559 subunit beta F, S 44 Thermosynechococcus elongatus Gene Name(s): psbF tsr1542
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center protein H H, W 65 Thermosynechococcus elongatus Gene Name(s): psbH tsl1386
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center protein I I, a 38 Thermosynechococcus elongatus Gene Name(s): psbI tsr1074
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center protein J J, b 39 Thermosynechococcus elongatus Gene Name(s): psbJ tsr1544
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center protein K K, c 37 Thermosynechococcus elongatus Gene Name(s): psbK tsl0176
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center protein L L, d 37 Thermosynechococcus elongatus Gene Name(s): psbL tsr1543
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center protein M M, e 36 Thermosynechococcus elongatus Gene Name(s): psbM tsl2052
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II manganese-stabilizing polypeptide O, f 246 Thermosynechococcus elongatus Gene Name(s): psbO tll0444
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center protein T T, g 32 Thermosynechococcus elongatus Gene Name(s): psbT tsr1531
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II 12 kDa extrinsic protein U, h 104 Thermosynechococcus elongatus Gene Name(s): psbU tll2409
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome c-550 V, i 137 Thermosynechococcus elongatus Gene Name(s): psbV tll1285
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center protein ycf12 m, y 46 Thermosynechococcus elongatus Gene Name(s): ycf12 tsr1242
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center protein X X, j 40 Thermosynechococcus elongatus Gene Name(s): psbX tsr2013
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center protein Y Y, k 28 Thermosynechococcus elongatus
Photosystem II reaction center protein Z Z, l 62 Thermosynechococcus elongatus Gene Name(s): psbZ tsr1967
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, F, G, N, Q, S 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, G, I, M, N, P, Q, R, a, e 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, G, J, Q, b 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, G 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

E, R, V, i 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

B, C, D, H, I, J, K, N, P, S, T, W, Z, a, b, c BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LMT
Query on LMT

B, D, I, M, N, Q, a, e DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OEC
Query on OEC

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

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

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

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

D, G 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
Y, k L-PEPTIDE LINKING C4 H9 N O2 --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.56 Å
  • R-Value Free: 0.385
  • R-Value Work: 0.366
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 130.78 α = 90.00
b = 227.76 β = 90.00
c = 308.63 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-05-23
  • Released Date: 2012-06-20
  • Deposition author(s): Kern, J., Alonso-Mori, R., Hellmich, J., Tran, R., Hattne, J., Laksmono, H., Gloeckner, C., Echols, N., Sierra, R.G., Sellberg, J., Lassalle-Kaiser, B., Gildea, R.J., Glatzel, P., Grosse-Kunstleve, R.W., Latimer, M.J., Mcqueen, T.A., Difiore, D., Fry, A.R., Messerschmidt, M.M., Miahnahri, A., Schafer, D.W., Seibert, M.M., Sokaras, D., Weng, T.-C., Zwart, P.H., White, W.E., Adams, P.D., Bogan, M.J., Boutet, S., Williams, G.J., Messinger, J., Sauter, N.K., Zouni, A., Bergmann, U., Yano, J., Yachandra, V.K.

Revision History

  • 2012-07-25
    Type: Non-polymer description
  • 2013-01-09
    Type: Database references
  • 2016-12-21
    Type: Data collection