MolNFT v1 · #170672 · protein
Plant psi-ferredoxin-plastocyanin supercomplex
6YEZ · Photosystem I P700 chlorophyll a apoprotein A1: “Plant psi-ferredoxin-plastocyanin supercomplex”. Electron microscopy, 16 ligands (CLA, BCR, LMG), 20 pockets (best druggability 0.82). MolNFT v1 #170672 on GenesisL1: 3D structure…
- PDB
- 6YEZ
- Type
- protein
- Length
- 3,438 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosystem I P700 chlorophyll a apoprotein A1; Photosystem I P700 chlorophyll a…
- EC
- 1.97.1.12
- UniProt
- A0A0F6NFW5, A0A0F6NGI2, P10793, P17227, E1C9L3, Q41038, Q32904, Q9SQL2, P09911, P16002
- Ligands
- CLA, BCR, LMG, CHL, LHG, DGD, LUT, SF4, PQN, XAT, CL0, 3PH, C7Z, FES, CA, CU
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 18 distinct chains · 51% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 743 | 61% helix, 4% strand | A0A0F6NFW5 |
| B | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 733 | 60% helix, 2% strand | A0A0F6NGI2 |
| C | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 10% helix, 21% strand | P10793 |
| D | Psad | protein | 143 | 18% helix, 24% strand | — |
| E | Psae | protein | 66 | 0% helix, 33% strand | — |
| F | Psaf | protein | 154 | 66% helix, 5% strand | — |
| G | Psag | protein | 97 | 61% helix, 4% strand | — |
| H | Psah | protein | 93 | 48% helix, 0% strand | — |
| I | Photosystem I reaction center subunit VIII | protein | 31 | 77% helix, 0% strand | P17227 |
| J | Psaj | protein | 42 | 67% helix, 2% strand | — |
| K | Photosystem I reaction center subunit X psak | protein | 81 | 51% helix, 4% strand | E1C9L3 |
| L | Psal | protein | 159 | 60% helix, 6% strand | — |
| 1 | LHCA1 | protein | 193 | 53% helix, 1% strand | — |
| 2 | Chlorophyll a-B binding protein, chloroplastic | protein | 208 | 50% helix, 1% strand | Q41038 |
| 3 | Chlorophyll a-B binding protein 3, chloroplastic | protein | 221 | 47% helix, 0% strand | Q32904 |
| 4 | Chlorophyll a-B binding protein P4, chloroplastic | protein | 198 | 53% helix, 1% strand | Q9SQL2 |
| N | Ferredoxin-1, chloroplastic | protein | 97 | 12% helix, 25% strand | P09911 |
| P | Plastocyanin, chloroplastic | protein | 99 | 3% helix, 31% strand | P16002 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 141 copies · chains A, F, J, B, 3, K, L, I, G, H, 1, 4, 2
- BCR · Beta-carotene · ligand · 27 copies · chains A, B, G, F, H, L, I, J, K, 3, 1, 4, 2
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 19 copies · chains K, A, B, 1, F, J, G, 4, 2, 3
- CHL · Chlorophyll B · ligand · 15 copies · chains G, 1, 4, 2, 3
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 8 copies · chains A, B, 1, 4, 2, 3
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 7 copies · chains B, C, F, 4, G, 1, J, A, 3
- LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 7 copies · chains A, J, 1, 2, 3, 4
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- PQN · Phylloquinone · ligand · 2 copies · chains A, J, B
- 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 · 2 copies · chains 2, F, 4
- CL0 · Chlorophyll A isomer · ligand · chains A, B
- 3PH · 1,2-diacyl-glycerol-3-sn-phosphate · ligand · chains 2, 4
- 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 · chains F, 1, 4
- FES · Fe2/s2 (inorganic) cluster · ligand · chains N
- CA · Calcium ion · metal · 2 copies · chains A, 3, B
- CU · Copper (II) ion · metal · chains P
- LMT · Dodecyl-beta-D-maltoside · additive · 6 copies · chains A, B, F, G, 3
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 | 855 | 0.82 | 0.84 | 70 | DGD |
| 2 | 984 | 0.80 | 0.82 | 96 | empty |
| 3 | 840 | 0.78 | 0.82 | 73 | empty |
| 4 | 775 | 0.76 | 0.80 | 83 | empty |
| 5 | 365 | 0.76 | 0.85 | 52 | CL0, CLA |
Interfaces
43 interfaces between chains.
- A–B · 3440 Ų buried · 36 hydrogen bonds · protein-protein
- H–L · 1935 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1640 Ų buried · 19 hydrogen bonds · protein-protein
- B–G · 1503 Ų buried · 18 hydrogen bonds · protein-protein
- A–F · 981 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6YEZ · Plant PSI-ferredoxin-plastocyanin supercomplex · the same entry in another collection · chain P against P, 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 A0A0F6NFW5
- Every structure of UniProt A0A0F6NGI2
- Every structure of UniProt P10793
- Every structure of UniProt P17227
- Every structure of UniProt E1C9L3
- Every structure of UniProt Q41038
- Every structure of UniProt Q32904
- Every structure of UniProt Q9SQL2
- Every structure of UniProt P09911
- Every structure of UniProt P16002
- Elsewhere: RCSB PDB 6YEZ · PDBe 6YEZ · UniProt A0A0F6NFW5 · UniProt A0A0F6NGI2 · UniProt P10793 · UniProt P17227 · UniProt E1C9L3 · UniProt Q41038 · UniProt Q32904 · UniProt Q9SQL2 · UniProt P09911 · UniProt P16002
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