MolNFT v1 · #177276 · protein
Structure of monomeric photosystem II
7EDA · Photosystem II protein D1: “Structure of monomeric photosystem II”. Electron microscopy, 15 ligands (CLA, BCR, DGD), 20 pockets (best druggability 0.86). MolNFT v1 #177276 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7EDA
- Type
- protein
- Length
- 2,567 residues
- Chains
- 20
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosystem II protein D1; Photosystem II CP47 reaction center protein; Photosystem II…
- EC
- 1.10.3.9
- UniProt
- P51765, D0VWR1, D0VWR7, D0VWR8, P12238, P12239, P19052, P12240, Q7DGD4, P19054, P12241, P12312, D0VWR2, P12313, P56152, P0A387, D0VWR3, D0VWR4, D0VWR5, P0DM37
- Ligands
- CLA, BCR, DGD, LHG, LMG, PHO, SQD, PL9, OEX, UNL, BCT, HEM, RRX, HEC, FE2
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 20 distinct chains · 50% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photosystem II protein D1 (EC 1.10.3.9) | protein | 334 | 57% helix, 4% strand | P51765 |
| B | Photosystem II CP47 reaction center protein | protein | 504 | 45% helix, 11% strand | D0VWR1 |
| C | Photosystem II CP43 reaction center protein | protein | 451 | 51% helix, 5% strand | D0VWR7 |
| D | Photosystem II D2 protein (EC 1.10.3.9) | protein | 341 | 58% helix, 4% strand | D0VWR8 |
| E | Cytochrome B559 subunit alpha | protein | 80 | 48% helix, 0% strand | P12238 |
| F | Cytochrome B559 subunit beta | protein | 34 | 68% helix, 0% strand | P12239 |
| H | Photosystem II reaction center protein H | protein | 62 | 52% helix, 6% strand | P19052 |
| I | Photosystem II reaction center protein I | protein | 32 | 66% helix, 0% strand | P12240 |
| J | Photosystem II reaction center protein J | protein | 36 | 58% helix, 0% strand | Q7DGD4 |
| K | Photosystem II reaction center protein K | protein | 37 | 59% helix, 0% strand | P19054 |
| L | Photosystem II reaction center protein L | protein | 30 | 73% helix, 3% strand | P12241 |
| M | Photosystem II reaction center protein M | protein | 30 | 73% helix, 0% strand | P12312 |
| O | Photosystem II manganese-stabilizing polypeptide | protein | 192 | 2% helix, 48% strand | D0VWR2 |
| T | Photosystem II reaction center protein T | protein | 29 | 59% helix, 0% strand | P12313 |
| U | Photosystem II 12 kda extrinsic protein | protein | 84 | 49% helix, 5% strand | P56152 |
| V | Cytochrome C-550 | protein | 135 | 40% helix, 7% strand | P0A387 |
| Y | Photosystem II reaction center protein YCF12 | protein | 27 | 70% helix, 0% strand | D0VWR3 |
| X | Photosystem II reaction center protein X | protein | 38 | 74% helix, 0% strand | D0VWR4 |
| Z | Photosystem II reaction center protein Z | protein | 57 | 68% helix, 0% strand | D0VWR5 |
| R | Photosystem II protein Y | protein | 34 | 76% helix, 0% strand | P0DM37 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 35 copies · chains A, D, L, I, B, H, M, C, K, Y, Z, X
- BCR · Beta-carotene · ligand · 8 copies · chains A, I, B, M, C, K, Z, D, F, J, Y
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 4 copies · chains A, C, J, D, V, B, H
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 4 copies · chains A, B, D, L, M, T, C
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 3 copies · chains A, C, I, B, L, M, D, F, J
- PHO · Pheophytin A · ligand · 2 copies · chains A, D
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 2 copies · chains A, C, D, K, E, F, X, R
- PL9 · 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 · ligand · 2 copies · chains A, D, F, X, L
- OEX · Ca-MN4-O5 cluster · ligand · chains A, C
- UNL · Unknown ligand · ligand · chains B
- BCT · Bicarbonate ion · ligand · chains A, D
- HEM · Protoporphyrin IX containing Fe · ligand · chains E, F, R
- RRX · (3R)-beta,beta-caroten-3-ol · ligand · chains H, X
- HEC · Heme C · ligand · chains C, V
- FE2 · Fe (II) ion · metal · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1114 | 0.86 | 0.87 | 94 | CLA, BCR |
| 2 | 767 | 0.85 | 0.88 | 78 | HEC |
| 3 | 544 | 0.81 | 0.87 | 47 | CLA |
| 4 | 1161 | 0.81 | 0.81 | 105 | CLA, DGD |
| 5 | 1129 | 0.81 | 0.81 | 106 | CLA, DGD |
Interfaces
63 interfaces between chains.
- A–D · 5421 Ų buried · 83 hydrogen bonds · protein-protein
- A–C · 3257 Ų buried · 50 hydrogen bonds · protein-protein
- B–D · 2964 Ų buried · 39 hydrogen bonds · protein-protein
- B–H · 1870 Ų buried · 31 hydrogen bonds · protein-protein
- D–E · 1393 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified, 2 cofactor, 1 disulfide (heme c attachment, formylation, disulfide, nonstandard).
Compared structures
- 7EDA · Structure of monomeric photosystem II · the same entry in another collection · chain L against L, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P51765
- Every structure of UniProt D0VWR1
- Every structure of UniProt D0VWR7
- Every structure of UniProt D0VWR8
- Every structure of UniProt P12238
- Every structure of UniProt P12239
- Every structure of UniProt P19052
- Every structure of UniProt P12240
- Every structure of UniProt Q7DGD4
- Every structure of UniProt P19054
- Every structure of UniProt P12241
- Every structure of UniProt P12312
- Every structure of UniProt D0VWR2
- Every structure of UniProt P12313
- Every structure of UniProt P56152
- Every structure of UniProt P0A387
- Every structure of UniProt D0VWR3
- Every structure of UniProt D0VWR4
- Every structure of UniProt D0VWR5
- Every structure of UniProt P0DM37
- Elsewhere: RCSB PDB 7EDA · PDBe 7EDA · UniProt P51765 · UniProt D0VWR1 · UniProt D0VWR7 · UniProt D0VWR8 · UniProt P12238 · UniProt P12239 · UniProt P19052 · UniProt P12240 · UniProt Q7DGD4 · UniProt P19054 · UniProt P12241 · UniProt P12312 · UniProt D0VWR2 · UniProt P12313 · UniProt P56152 · UniProt P0A387 · UniProt D0VWR3 · UniProt D0VWR4 · UniProt D0VWR5 · UniProt P0DM37
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