MolNFT v1 · #185179 · protein
Unstacked compact dunaliella psii
7PI0 · Photosystem II protein D1: “Unstacked compact dunaliella psii”. Electron microscopy, 28 ligands (CLA, CHL, LHG), 20 pockets (best druggability 0.87). MolNFT v1 #185179 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7PI0
- Type
- protein
- Length
- 7,442 residues
- Chains
- 50
- 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
- D0FY08, A0A1C8XRM6, D0FY13, D0FXY3, A0A1C8XRK9, D0FY01, A0A1C8XRP4, A0A1C8XRP3, D0FXX5, A0A1C8XRM8, D0FXX2, D0FY19, D0FY04, D0FXZ2, A1XKU7
- Ligands
- CLA, CHL, LHG, LUT, BCR, LMG, SQD, NEX, DGD, XAT, 3PH, DGA, PHO, SPH, 4RF, PTY…
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 25 distinct chains · 50% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a | Photosystem II protein D1 (EC 1.10.3.9) | protein | 336 | 58% helix, 4% strand | D0FY08 |
| B, b | Photosystem II CP47 reaction center protein | protein | 484 | 48% helix, 11% strand | A0A1C8XRM6 |
| V, v | Photosystem II reaction center protein YCF12 | protein | 32 | 81% helix, 0% strand | D0FY13 |
| C, c | Photosystem II CP43 reaction center protein | protein | 449 | 56% helix, 5% strand | D0FXY3 |
| D, d | Photosystem II D2 protein (EC 1.10.3.9) | protein | 348 | 62% helix, 3% strand | A0A1C8XRK9 |
| E, e | Cytochrome B559 subunit alpha | protein | 76 | 49% helix, 0% strand | D0FY01 |
| F, f | Cytochrome B559 subunit beta | protein | 31 | 77% helix, 3% strand | A0A1C8XRP4 |
| H, h | Photosystem II reaction center protein H | protein | 67 | 52% helix, 4% strand | A0A1C8XRP3 |
| I, i | Photosystem II reaction center protein I | protein | 35 | 74% helix, 0% strand | D0FXX5 |
| J, j | Photosystem II reaction center protein J | protein | 36 | 58% helix, 0% strand | A0A1C8XRM8 |
| K, k | Photosystem II reaction center protein K | protein | 37 | 68% helix, 0% strand | D0FXX2 |
| L, l | Photosystem II reaction center protein L | protein | 38 | 61% helix, 3% strand | D0FY19 |
| M, m | Psbm | protein | 31 | 84% helix, 0% strand | — |
| O, o | Psbo | protein | 238 | 8% helix, 43% strand | — |
| P, p | Psbp | protein | 187 | 18% helix, 36% strand | — |
| T, t | Photosystem II reaction center protein T | protein | 30 | 70% helix, 0% strand | D0FY04 |
| W, w | Psbw | protein | 44 | 52% helix, 0% strand | — |
| X, x | Psbx | protein | 30 | 83% helix, 0% strand | — |
| Z, z | Photosystem II reaction center protein Z | protein | 61 | 84% helix, 0% strand | D0FXZ2 |
| N, n | Lhcii M3 | protein | 222 | 51% helix, 2% strand | — |
| G, g | Chlorophyll a-B binding protein, chloroplastic | protein | 221 | 49% helix, 2% strand | A1XKU7 |
| R, r | CP29 | protein | 196 | 44% helix, 7% strand | — |
| S, s | CP26 | protein | 243 | 45% helix, 2% strand | — |
| Y, y | Lhcii M1 | protein | 222 | 53% helix, 3% strand | — |
| U, u | Psbu | protein | 27 | 44% helix, 0% strand | — |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 156 copies · chains A, D, T, L, I, W, B, H, R, M, m, C, S, K, V, Z, X, N, Y, G, r, a, d, l, t, i, w, b, h, c, s, k, v, z, x, n, y, g
- CHL · Chlorophyll B · ligand · 46 copies · chains N, G, S, Y, R, B, r, n, g, s, y, b
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 18 copies · chains C, Z, S, A, B, D, L, T, M, N, G, Y, c, z, s, a, b, d, l, t, m, n, g, y
- LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 18 copies · chains N, G, R, S, Y, n, g, r, s, y
- BCR · Beta-carotene · ligand · 16 copies · chains A, I, B, M, t, C, K, Z, S, V, J, D, F, a, i, T, b, m, c, k, z, s, v, j, d, f
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 14 copies · chains A, C, I, W, B, D, L, M, V, J, K, F, H, Y, a, c, i, w, b, d, l, m, v, j, k, y, f, h
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 10 copies · chains A, C, D, K, B, L, l, m, t, a, o, M, c, d, k, T, b, O
- NEX · (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R, 6R)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13, 15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol · ligand · 10 copies · chains N, G, H, R, S, Y, n, s, g, h, r, y
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 8 copies · chains B, R, A, C, J, D, b, r, a, c, j, d
- XAT · (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-tetrahydro-beta,beta-carotene-3,3'-diol · ligand · 8 copies · chains N, Y, G, R, n, y, g, r
- 3PH · 1,2-diacyl-glycerol-3-sn-phosphate · ligand · 6 copies · chains B, M, t, A, T, b, S, m, a, s
- DGA · Diacyl glycerol · ligand · 6 copies · chains B, D, H, C, I, W, V, J, b, d, h, x, c, i, w, v, j
- PHO · Pheophytin A · ligand · 4 copies · chains A, D, a, d
- SPH · Sphingosine · ligand · 4 copies · chains A, I, C, a, i, c
- 4RF · Tripalmitoylglycerol · ligand · 4 copies · chains I, W, r, A, C, E, J, K, R, i, w, c, e, j, k
- PTY · Phosphatidylethanolamine · ligand · 4 copies · chains C, N, Y, c, n, y
- OEX · Ca-MN4-O5 cluster · ligand · 2 copies · chains A, C, a, c
- C7Z · (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E}, 9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol · ligand · 2 copies · chains B, R, t, T, b, r
- LMK · trimethyl-[(2~{R})-1-oxidanyl-1-oxidanylidene-4-[(2~{S})-2-[(1~{S})-1-oxidanyloctadecoxy]-3-[(1~{R})-1-oxidanyloctadecoxy]propoxy]butan-2-yl]azanium · ligand · 2 copies · chains C, S, c, s
- BCT · Bicarbonate ion · ligand · 2 copies · chains A, D, 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 · 2 copies · chains A, D, L, T, a, d, l, t
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains E, F, e, f
- RRX · (3R)-beta,beta-caroten-3-ol · ligand · 2 copies · chains B, H, X, b, h, x
- ERG · Ergosterol · ligand · 2 copies · chains R, i, w, I, W, r
- LPX · (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate · ligand · 2 copies · chains C, S, c, s
- FE2 · Fe (II) ion · metal · 2 copies · chains A, D, a, d
- NA · Sodium ion · metal · 2 copies · chains A, D, a, d
- CL · Chloride ion · ion · 4 copies · chains A, D, C, a, d, c
- LMT · Dodecyl-beta-D-maltoside · additive · 2 copies · chains B, b
- GOL · Glycerol · additive · chains I, r
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 | 1024 | 0.87 | 0.88 | 90 | CLA, BCR |
| 2 | 926 | 0.87 | 0.87 | 75 | BCR |
| 3 | 1049 | 0.86 | 0.86 | 110 | CLA, LMG |
| 4 | 1019 | 0.85 | 0.86 | 112 | CLA, LMG |
| 5 | 1153 | 0.84 | 0.85 | 118 | empty |
Interfaces
159 interfaces between chains.
- a–d · 5470 Ų buried · 70 hydrogen bonds · protein-protein
- A–D · 5456 Ų buried · 67 hydrogen bonds · protein-protein
- a–c · 3343 Ų buried · 53 hydrogen bonds · protein-protein
- A–C · 3337 Ų buried · 44 hydrogen bonds · protein-protein
- B–D · 2717 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation, phosphorylation).
Compared structures
- 7PI0 · Unstacked compact Dunaliella PSII · the same entry in another collection · chain c against c, 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 D0FY08
- Every structure of UniProt A0A1C8XRM6
- Every structure of UniProt D0FY13
- Every structure of UniProt D0FXY3
- Every structure of UniProt A0A1C8XRK9
- Every structure of UniProt D0FY01
- Every structure of UniProt A0A1C8XRP4
- Every structure of UniProt A0A1C8XRP3
- Every structure of UniProt D0FXX5
- Every structure of UniProt A0A1C8XRM8
- Every structure of UniProt D0FXX2
- Every structure of UniProt D0FY19
- Every structure of UniProt D0FY04
- Every structure of UniProt D0FXZ2
- Every structure of UniProt A1XKU7
- Elsewhere: RCSB PDB 7PI0 · PDBe 7PI0 · UniProt D0FY08 · UniProt A0A1C8XRM6 · UniProt D0FY13 · UniProt D0FXY3 · UniProt A0A1C8XRK9 · UniProt D0FY01 · UniProt A0A1C8XRP4 · UniProt A0A1C8XRP3 · UniProt D0FXX5 · UniProt A0A1C8XRM8 · UniProt D0FXX2 · UniProt D0FY19 · UniProt D0FY04 · UniProt D0FXZ2 · UniProt A1XKU7
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