MolNFT v1 · #187344 · protein
Structure of a monomeric photosystem II core complex from a cyanobacterium acclimated to far-red light
7SA3 · Photosystem Q(B) protein: “Structure of a monomeric photosystem II core complex from a cyanobacterium acclimated to far-red light”. Electron microscopy, 13 ligands (CLA, BCR, F6C), 20 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 7SA3
- Type
- protein
- Length
- 1,667 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosystem Q(B) protein; Photosystem II CP47 reaction center protein; Photosystem II…
- EC
- 1.10.3.9
- UniProt
- B4WKH9, B4WKI1, B4WKI2, B4WKI3, B4WII1, B4WKJ2, B4WM03, B4WR12
- Ligands
- CLA, BCR, F6C, PHO, DGD, LMG, CL7, PL9, LHG, HEM, CA, FE2, CL
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 9 distinct chains · 59% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photosystem Q(B) protein | protein | 303 | 63% helix, 3% strand | B4WKH9 |
| B | Photosystem II CP47 reaction center protein | protein | 450 | 50% helix, 10% strand | B4WKI1 |
| C | Photosystem II CP43 reaction center protein | protein | 420 | 58% helix, 5% strand | B4WKI2 |
| D | Photosystem II D2 protein (EC 1.10.3.9) | protein | 336 | 60% helix, 3% strand | B4WKI3 |
| E | Cytochrome B559 subunit alpha | protein | 41 | 61% helix, 0% strand | B4WII1 |
| F | Cytochrome B559 subunit beta | protein | 30 | 73% helix, 0% strand | B4WKJ2 |
| I | Photosystem II reaction center protein I | protein | 27 | 85% helix, 0% strand | B4WM03 |
| K | Photosystem II reaction center protein K | protein | 37 | 70% helix, 0% strand | B4WR12 |
| N | Unknown | protein | 23 | 74% helix, 0% strand | — |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 28 copies · chains A, D, I, B, C, K, N
- BCR · Beta-carotene · ligand · 5 copies · chains A, I, B, C, K, D, F
- F6C · Chlorophyll F · ligand · 4 copies · chains B, D, C
- PHO · Pheophytin A · ligand · 2 copies · chains A, D
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 2 copies · chains B, D, A, C
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 2 copies · chains B, D, F, N
- CL7 · Chlorophyll D · ligand · chains A, D
- 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 · chains A, D
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · chains A, C, D, N
- HEM · Protoporphyrin IX containing Fe · ligand · chains E, F
- CA · Calcium ion · metal · chains A, C
- FE2 · Fe (II) ion · metal · chains A, D
- CL · Chloride ion · ion · chains A, D
- LMT · Dodecyl-beta-D-maltoside · additive · 6 copies · chains A, D, C, N, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1199 | 0.83 | 0.83 | 99 | CLA, PHO |
| 2 | 715 | 0.82 | 0.85 | 105 | CA, CL, LMT |
| 3 | 1060 | 0.80 | 0.81 | 106 | CLA, DGD |
| 4 | 489 | 0.73 | 0.82 | 62 | LHG |
| 5 | 276 | 0.67 | 0.82 | 33 | empty |
Interfaces
17 interfaces between chains.
- A–D · 4877 Ų buried · 60 hydrogen bonds · protein-protein
- B–D · 2426 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 2405 Ų buried · 26 hydrogen bonds · protein-protein
- C–K · 836 Ų buried · 5 hydrogen bonds · protein-protein
- A–I · 725 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7SA3 · Structure of a monomeric photosystem II core complex from a cyanobacterium acclimated to… · the same entry in another collection · chain A against A, 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 B4WKH9
- Every structure of UniProt B4WKI1
- Every structure of UniProt B4WKI2
- Every structure of UniProt B4WKI3
- Every structure of UniProt B4WII1
- Every structure of UniProt B4WKJ2
- Every structure of UniProt B4WM03
- Every structure of UniProt B4WR12
- Elsewhere: RCSB PDB 7SA3 · PDBe 7SA3 · UniProt B4WKH9 · UniProt B4WKI1 · UniProt B4WKI2 · UniProt B4WKI3 · UniProt B4WII1 · UniProt B4WKJ2 · UniProt B4WM03 · UniProt B4WR12
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