Research workbench
Organization and energy transfer in a huge diatom psi-fcpi supercomplex
Analyse Organization and energy transfer in a huge diatom psi-fcpi supercomplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LY5
- Type
- protein
- Length
- 6,644 residues
- Chains
- 36
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fcpi-7; Fcpi-1; Fcpi-11; Fcpi-6; Fcpi-5; Fcpi-8; Fcpi-4; Fcpi-10; Fcpi-3; Fcpi-9…
- Ligands
- CLA, A86, DD6, KC1, LHG, BCR, LMG, DGD, SF4, SQD, PQN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 34 distinct chains · 51% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fcpi-7 | protein | 168 | 46% helix, 1% strand | — |
| B | Fcpi-1 | protein | 132 | 63% helix, 5% strand | — |
| C | Fcpi-11 | protein | 163 | 48% helix, 1% strand | — |
| D | Fcpi-6 | protein | 172 | 53% helix, 0% strand | — |
| E | Fcpi-5 | protein | 188 | 57% helix, 2% strand | — |
| F | Fcpi-8 | protein | 180 | 50% helix, 1% strand | — |
| G | Fcpi-4 | protein | 214 | 44% helix, 1% strand | — |
| H | Fcpi-10 | protein | 170 | 52% helix, 1% strand | — |
| I | Fcpi-3 | protein | 161 | 57% helix, 0% strand | — |
| J | Fcpi-9 | protein | 167 | 51% helix, 1% strand | — |
| K | Fcpi-13 | protein | 169 | 49% helix, 1% strand | — |
| L | Fcpi-14 | protein | 196 | 48% helix, 2% strand | — |
| M | Fcpi-16 | protein | 187 | 47% helix, 0% strand | — |
| N | Fcpi-21 | protein | 219 | 42% helix, 0% strand | — |
| O, P, Q | Fcpi | protein | 173 | 47% helix, 0% strand | — |
| R | Fcpi-24 | protein | 211 | 45% helix, 1% strand | — |
| S | Fcpi-23 | protein | 220 | 41% helix, 0% strand | — |
| T | Fcpi-12 | protein | 172 | 52% helix, 2% strand | — |
| W | Fcpi-17 | protein | 160 | 44% helix, 1% strand | — |
| X | Fcpi-17 | protein | 161 | 47% helix, 1% strand | — |
| a | Psaa | protein | 742 | 61% helix, 5% strand | — |
| b | Psab | protein | 732 | 60% helix, 2% strand | — |
| c | Psac | protein | 80 | 21% helix, 20% strand | — |
| d | Psad | protein | 132 | 17% helix, 23% strand | — |
| e | Psae | protein | 63 | 5% helix, 37% strand | — |
| f | Psaf | protein | 162 | 61% helix, 5% strand | — |
| i | Psai | protein | 33 | 73% helix, 0% strand | — |
| j | Psaj | protein | 41 | 71% helix, 2% strand | — |
| l | Psal | protein | 144 | 58% helix, 3% strand | — |
| m | Psam | protein | 28 | 89% helix, 0% strand | — |
| g | Psas | protein | 134 | 31% helix, 0% strand | — |
| h | Psar | protein | 89 | 72% helix, 0% strand | — |
| U | Fcpi-2 | protein | 156 | 47% helix, 1% strand | — |
| V | Fcpi-19 | protein | 179 | 53% helix, 2% strand | — |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 326 copies · chains A, D, V, f, B, l, U, C, H, b, E, M, a, G, F, h, J, K, L, I, T, N, Q, R, O, P, S, W, X, j, i, m, d
- 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 · 102 copies · chains A, V, B, C, b, m, D, E, G, a, F, J, K, H, I, L, Q, M, N, O, P, R, S, T, U, W, X, h
- DD6 · (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol · ligand · 35 copies · chains A, D, B, C, l, E, M, G, F, K, H, I, J, L, O, P, Q, R, S, W, a, j
- KC1 · Chlorophyll c1 · ligand · 34 copies · chains A, B, C, D, E, F, O, G, L, I, K, H, J, Q, M, N, P, R, S, T, W, X, U, V
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 22 copies · chains D, E, a, F, J, G, P, I, T, O, Q, M, R, l, b, h, A, f, V, i, m, j, B
- BCR · Beta-carotene · ligand · 18 copies · chains a, b, h, C, f, F, i, l, j, U, B, m
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 16 copies · chains D, a, j, E, G, M, I, F, J, K, L, A, f, b, i, m, H, h, V
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 3 copies · chains C, H, G, L, b, g
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains a, b, c
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 2 copies · chains A, H, b, h
- PQN · Phylloquinone · ligand · 2 copies · chains a, b, i
- LMT · Dodecyl-beta-D-maltoside · additive · 26 copies · chains B, i, m, l, E, a, F, G, I, P, K, L, Q, j, H, b, h, U
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 | 1006 | 0.83 | 0.84 | 78 | DGD |
| 2 | 574 | 0.80 | 0.85 | 60 | CLA |
| 3 | 462 | 0.73 | 0.83 | 50 | empty |
| 4 | 509 | 0.72 | 0.81 | 56 | empty |
| 5 | 899 | 0.72 | 0.76 | 87 | A86, CLA |
Interfaces
88 interfaces between chains.
- a–b · 3503 Ų buried · 44 hydrogen bonds · protein-protein
- c–d · 1535 Ų buried · 17 hydrogen bonds · protein-protein
- d–g · 1226 Ų buried · 9 hydrogen bonds · protein-protein
- b–f · 1148 Ų buried · 11 hydrogen bonds · protein-protein
- a–f · 1030 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 128 covalent, 1 disulfide (covalent ligand, additive adduct, disulfide).
Compared structures
- 6LY5 · Organization and energy transfer in a huge diatom PSI-FCPI supercomplex · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 6LY5 · PDBe 6LY5
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