MolNFT v1 · #156255 · protein
Organization and energy transfer in a huge diatom psi-fcpi supercomplex
6LY5 · Fcpi-7: “Organization and energy transfer in a huge diatom psi-fcpi supercomplex”. Electron microscopy, 11 ligands (CLA, A86, DD6), 20 pockets (best druggability 0.83). MolNFT v1 #156255 on GenesisL1: 3D structure, binding sites and…
- 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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