MolNFT v1 · #183185 · protein
Structure of psii-M
7NHO · Photosystem II protein D1 1: “Structure of psii-M”. Electron microscopy, 11 ligands (CLA, BCR, LMG), 20 pockets (best druggability 0.84). MolNFT v1 #183185 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7NHO
- Type
- protein
- Length
- 2,086 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosystem II protein D1 1; Photosystem II CP47 reaction center protein; Photosystem II…
- EC
- 1.10.3.9
- UniProt
- P0A444, Q8DIQ1, Q8DIF8, Q8CM25, Q8DIP0, Q8DIN9, Q8DJ43, Q8DJZ6, Q9F1K9, Q8DIN8, Q8DHA7, Q8DIQ0, Q9F1R6, Q8DJI1, Q8DHJ2
- Ligands
- CLA, BCR, LMG, PHO, LHG, BCT, PL9, HEM, FE, MN, CL
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 15 distinct chains · 55% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photosystem II protein D1 1 (EC 1.10.3.9) | protein | 335 | 58% helix, 4% strand | P0A444 |
| B | Photosystem II CP47 reaction center protein | protein | 485 | 45% helix, 11% strand | Q8DIQ1 |
| C | Photosystem II CP43 reaction center protein | protein | 448 | 51% helix, 4% strand | Q8DIF8 |
| D | Photosystem II D2 protein (EC 1.10.3.9) | protein | 340 | 61% helix, 2% strand | Q8CM25 |
| E | Cytochrome B559 subunit alpha | protein | 77 | 55% helix, 0% strand | Q8DIP0 |
| F | Cytochrome B559 subunit beta | protein | 38 | 53% helix, 0% strand | Q8DIN9 |
| H | Photosystem II reaction center protein H | protein | 65 | 48% helix, 2% strand | Q8DJ43 |
| I | Photosystem II reaction center protein I | protein | 35 | 74% helix, 0% strand | Q8DJZ6 |
| K | Photosystem II reaction center protein K | protein | 37 | 65% helix, 0% strand | Q9F1K9 |
| L | Photosystem II reaction center protein L | protein | 37 | 59% helix, 3% strand | Q8DIN8 |
| M | Photosystem II reaction center protein M | protein | 34 | 76% helix, 0% strand | Q8DHA7 |
| T | Photosystem II reaction center protein T | protein | 30 | 67% helix, 0% strand | Q8DIQ0 |
| X | Photosystem II reaction center X protein | protein | 35 | 86% helix, 0% strand | Q9F1R6 |
| y | Photosystem II reaction center protein YCF12 | protein | 28 | 64% helix, 0% strand | Q8DJI1 |
| Z | Photosystem II reaction center protein Z | protein | 62 | 76% helix, 0% strand | Q8DHJ2 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 35 copies · chains A, D, T, L, I, B, H, M, X, C, K, y, Z
- BCR · Beta-carotene · ligand · 10 copies · chains A, I, B, M, C, K, Z, D, F, H, X, y
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 7 copies · chains A, B, D, L, M, C, K, Z, F, T, I
- PHO · Pheophytin A · ligand · 2 copies · chains A, D
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 2 copies · chains A, C, D
- BCT · Bicarbonate ion · 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, L, T
- HEM · Protoporphyrin IX containing Fe · ligand · chains E, F
- FE · Fe (III) ion · metal · chains A, D
- MN · Manganese (II) ion · metal · chains A
- CL · Chloride ion · ion · 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1095 | 0.84 | 0.84 | 77 | CLA, BCR |
| 2 | 878 | 0.83 | 0.85 | 97 | LMG |
| 3 | 1069 | 0.82 | 0.83 | 121 | MN, CL |
| 4 | 1121 | 0.80 | 0.81 | 109 | CLA |
| 5 | 1106 | 0.78 | 0.79 | 81 | CLA |
Interfaces
36 interfaces between chains.
- A–D · 5530 Ų buried · 47 hydrogen bonds · protein-protein
- A–C · 3046 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 2637 Ų buried · 23 hydrogen bonds · protein-protein
- B–H · 2038 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1290 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7NHO · Structure of PSII-M · 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 P0A444
- Every structure of UniProt Q8DIQ1
- Every structure of UniProt Q8DIF8
- Every structure of UniProt Q8CM25
- Every structure of UniProt Q8DIP0
- Every structure of UniProt Q8DIN9
- Every structure of UniProt Q8DJ43
- Every structure of UniProt Q8DJZ6
- Every structure of UniProt Q9F1K9
- Every structure of UniProt Q8DIN8
- Every structure of UniProt Q8DHA7
- Every structure of UniProt Q8DIQ0
- Every structure of UniProt Q9F1R6
- Every structure of UniProt Q8DJI1
- Every structure of UniProt Q8DHJ2
- Elsewhere: RCSB PDB 7NHO · PDBe 7NHO · UniProt P0A444 · UniProt Q8DIQ1 · UniProt Q8DIF8 · UniProt Q8CM25 · UniProt Q8DIP0 · UniProt Q8DIN9 · UniProt Q8DJ43 · UniProt Q8DJZ6 · UniProt Q9F1K9 · UniProt Q8DIN8 · UniProt Q8DHA7 · UniProt Q8DIQ0 · UniProt Q9F1R6 · UniProt Q8DJI1 · UniProt Q8DHJ2
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