MolNFT v2 · #213843 · protein
Structural insights into photosystem II supercomplex and trimeric FCP antennae of a centric diatom Cyclotella meneghiniana
8J5K · PsbA: “Structural insights into photosystem II supercomplex and trimeric FCP antennae of a centric diatom Cyclotella…”. Electron microscopy at 2.93, 16 ligands (CLA, A86, LMG), 20 pockets (best druggability 0.87). MolNFT v2 #213843…
- PDB
- 8J5K
- Type
- protein
- Length
- 7,682 residues
- Chains
- 56
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.93
- Source
- Stephanocyclus meneghinianus
- Molecule
- PsbA; PsbB; PsbC; PsbD; PsbE; PsbF; PsbH; PsbI; PsbJ; PsbK; PsbL; PsbM; Psb34; PsbO…
- Ligands
- CLA, A86, LMG, BCR, LHG, DD6, SQD, PHO, PL9, HEM, OEX, BCT, ET4, DGD, FE2, CL
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · resolution 2.93 · 28 distinct chains · 52% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a | PsbA | protein | 333 | 58% helix, 5% strand | — |
| B, b | PsbB | protein | 481 | 50% helix, 9% strand | — |
| C, c | PsbC | protein | 450 | 55% helix, 4% strand | — |
| D, d | PsbD | protein | 340 | 60% helix, 2% strand | — |
| E, e | PsbE | protein | 75 | 48% helix, 0% strand | — |
| F, f | PsbF | protein | 31 | 81% helix, 0% strand | — |
| H, h | PsbH | protein | 65 | 51% helix, 2% strand | — |
| I, i | PsbI | protein | 34 | 65% helix, 0% strand | — |
| J, j | PsbJ | protein | 34 | 71% helix, 0% strand | — |
| K, k | PsbK | protein | 37 | 65% helix, 0% strand | — |
| L, l | PsbL | protein | 37 | 62% helix, 3% strand | — |
| M, m | PsbM | protein | 41 | 73% helix, 0% strand | — |
| N, n | Psb34 | protein | 30 | 40% helix, 0% strand | — |
| O, o | PsbO | protein | 248 | 6% helix, 42% strand | — |
| Q, q | PsbQ' | protein | 145 | 55% helix, 0% strand | — |
| T, t | PsbT | protein | 29 | 72% helix, 0% strand | — |
| U, u | PsbU | protein | 92 | 37% helix, 4% strand | — |
| V, v | PsbV | protein | 136 | 47% helix, 6% strand | — |
| W, w | PsbW | protein | 50 | 42% helix, 0% strand | — |
| X, x | PsbX | protein | 34 | 85% helix, 0% strand | — |
| Y, y | PsbY | protein | 33 | 79% helix, 0% strand | — |
| Z, z | PsbZ | protein | 59 | 88% helix, 0% strand | — |
| 5, 0 | FCPII-G, fucoxanthin chlorophyll a/c binding protein | protein | 169 | 57% helix, 0% strand | — |
| 7, 2 | FCPII-H2, fucoxanthin chlorophyll a/c binding protein | protein | 164 | 46% helix, 0% strand | — |
| 6, 1 | FCPII-H1, fucoxanthin chlorophyll a/c binding protein | protein | 164 | 49% helix, 0% strand | — |
| p, P | FCPII-I, fucoxanthin chlorophyll a/c binding protein | protein | 214 | 46% helix, 0% strand | — |
| 4, 9 | FCPII-K, fucoxanthin chlorophyll a/c binding protein | protein | 153 | 55% helix, 0% strand | — |
| 3, 8 | FCPII-J, fucoxanthin chlorophyll a/c binding protein | protein | 163 | 52% helix, 1% strand | — |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 206 copies · chains A, D, I, W, B, H, N, L, M, t, C, K, Y, Z, X, a, d, i, w, b, h, n, T, l, m, c, k, y, z, x, 5, 6, 7, p, 4, 3, P, 9, 8, 0, 1, 2
- A86 · (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate · ligand · 24 copies · chains 5, 6, 7, p, 4, 3, P, 9, 8, 0, 1, 2
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 22 copies · chains B, N, C, D, F, J, H, Q, Y, L, M, t, m, A, I, W, K, b, n, c, d, f, j, h, q, y, T, l, a, i, w, k, 5, 0
- BCR · Beta-carotene · ligand · 20 copies · chains A, I, B, M, t, N, C, K, Z, D, F, J, H, X, 0, Y, a, i, T, b, m, n, c, k, z, d, f, j, h, x, 5, y
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 14 copies · chains A, B, D, L, C, M, T, X, 0, H, a, b, d, l, c, m, t, x, 5, h
- DD6 · (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol · ligand · 12 copies · chains 7, 6, p, 3, P, 8, 2, 1
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 8 copies · chains A, C, D, K, T, b, B, a, t, N, i, c, d, k, I, n, 5, 6, 0, 1
- PHO · Pheophytin A · ligand · 4 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 · 4 copies · chains A, D, L, T, a, d, l, t
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains E, F, C, V, e, f, c, v
- OEX · Ca-MN4-O5 cluster · ligand · 2 copies · chains A, C, a, c
- BCT · Bicarbonate ion · ligand · 2 copies · chains A, D, a, d
- ET4 · (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol · ligand · 2 copies · chains 5, 0
- DGD · Digalactosyl diacyl glycerol (dgdg) · sugar · 8 copies · chains A, C, J, D, B, H, a, c, j, d, b, h
- FE2 · Fe (II) ion · metal · 2 copies · chains A, D, a, d
- CL · Chloride ion · ion · 2 copies · chains A, C, a, c
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 | 986 | 0.87 | 0.88 | 103 | DGD |
| 2 | 962 | 0.87 | 0.88 | 91 | HEM |
| 3 | 897 | 0.86 | 0.88 | 86 | DGD |
| 4 | 1163 | 0.86 | 0.87 | 87 | HEM |
| 5 | 801 | 0.85 | 0.88 | 90 | empty |
Interfaces
183 interfaces between chains.
- a–d · 5297 Ų buried · 48 hydrogen bonds · protein-protein
- A–D · 5272 Ų buried · 48 hydrogen bonds · protein-protein
- a–c · 3093 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 3093 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 2530 Ų buried · 28 hydrogen bonds · protein-protein
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 8J5K · PDBe 8J5K
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