Research workbench
Structure of low-light grown chlorella ohadii photosystem I
Analyse Structure of low-light grown chlorella ohadii photosystem I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZZX
- Type
- protein
- Length
- 4,684 residues
- Chains
- 24
- 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
- W8SY74, W8SUA3, W8SKM2, A0A2P6TKF8, A0A2P6U4S6, A0A2P6TPV8, A0A2P6TZI8, A0A2P6TPU7, W8SUD1, A0A2P6U0J1, A0A2P6TC44, W8SU98, W8SIP9, A0A2P6THB2, A0A2P6TT36, A0A2P6TMT4, A0A2P6U4K1, A0A2P6TPR7, A0A2P6TZ50, A0A2P6TMX4, A0A2P6TMI2
- Ligands
- CLA, CHL, BCR, LHG, LUT, PTY, PLM, SQD, DGD, PCW, SPH, OLA, DGA, XAT, SF4, PQN…
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 23 distinct chains · 54% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 741 | 60% helix, 5% strand | W8SY74 |
| B | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 731 | 62% helix, 3% strand | W8SUA3 |
| C | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 16% helix, 20% strand | W8SKM2 |
| D | Photosystem I reaction center subunit chloroplastic | protein | 143 | 20% helix, 24% strand | A0A2P6TKF8 |
| E | Photosystem I reaction center subunit IV | protein | 64 | 5% helix, 36% strand | A0A2P6U4S6 |
| F | Psi-F | protein | 165 | 64% helix, 5% strand | A0A2P6TPV8 |
| G | Photosystem I reaction center subunit chloroplastic | protein | 99 | 64% helix, 4% strand | A0A2P6TZI8 |
| H | Photosystem I reaction center subunit VI-chloroplastic- like | protein | 94 | 44% helix, 1% strand | A0A2P6TPU7 |
| J | Photosystem I reaction center subunit IX | protein | 41 | 71% helix, 2% strand | W8SUD1 |
| K | Photosystem I reaction center subunit chloroplastic | protein | 86 | 48% helix, 3% strand | A0A2P6U0J1 |
| L | Photosystem I reaction center subunit XI | protein | 157 | 57% helix, 6% strand | A0A2P6TC44 |
| M | Photosystem I reaction center subunit XII | protein | 31 | 84% helix, 0% strand | W8SU98 |
| I | Photosystem I reaction center subunit VIII | protein | 35 | 71% helix, 0% strand | W8SIP9 |
| O | Photosystem I subunit O | protein | 87 | 59% helix, 0% strand | A0A2P6THB2 |
| 1, a | Chlorophyll a-B binding protein, chloroplastic | protein | 192 | 52% helix, 2% strand | A0A2P6TT36 |
| 3 | Glutathione reductase | protein | 241 | 49% helix, 1% strand | A0A2P6TMT4 |
| 4 | LHCA4 | protein | 207 | 50% helix, 1% strand | — |
| 5 | Chlorophyll a-B binding protein, chloroplastic | protein | 229 | 45% helix, 5% strand | A0A2P6U4K1 |
| 6 | Chlorophyll a-B binding protein, chloroplastic | protein | 231 | 44% helix, 7% strand | A0A2P6TPR7 |
| 7 | LHCA7 | protein | 221 | 55% helix, 0% strand | — |
| 8 | Chlorophyll a-B binding protein, chloroplastic | protein | 219 | 53% helix, 0% strand | A0A2P6TZ50 |
| 2 | Chlorophyll a-B binding protein, chloroplastic | protein | 215 | 58% helix, 1% strand | A0A2P6TMX4 |
| 9 | Chlorophyll a-B binding protein, chloroplastic | protein | 183 | 59% helix, 1% strand | A0A2P6TMI2 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 208 copies · chains A, B, J, 3, K, O, L, H, I, F, M, 2, G, 9, 1, 7, 8, a, 4, 5, 6
- CHL · Chlorophyll B · ligand · 47 copies · chains A, 3, 1, G, 8, a, 4, 5, 6, 7, F, 2, 9, B
- BCR · Beta-carotene · ligand · 32 copies · chains A, O, B, G, 9, F, J, H, L, K, I, 3, 5, 4, 6, 7, 8
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 24 copies · chains A, 3, B, 1, F, J, 7, 8, a, 4, 6, 5, 2, 9, M
- LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 21 copies · chains 1, G, a, 3, 4, 5, 6, 7, 8, 2, 9
- PTY · Phosphatidylethanolamine · ligand · 11 copies · chains A, 7, B, F, J, G, 1, a, 3, 5, 4, 2, 9
- PLM · Palmitic acid · ligand · 7 copies · chains a, 4, 8, 5, 6, 7, 1
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 5 copies · chains A, B, G, 9, H, L, 2, M, I, 6, 7
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 4 copies · chains B, C, 3, 5, 4, F, 8
- PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 4 copies · chains A, F, K, 3, 6, 7
- SPH · Sphingosine · ligand · 4 copies · chains J, 4, 5, 6, B, 9
- OLA · Oleic acid · ligand · 4 copies · chains 1, a, 8
- DGA · Diacyl glycerol · ligand · 4 copies · chains 7, 5, 4, 8, 2
- 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 · 4 copies · chains 7, 2, 9
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- PQN · Phylloquinone · ligand · 2 copies · chains A, B
- RRX · (3R)-beta,beta-caroten-3-ol · ligand · 2 copies · chains A, J, 3
- AXT · Astaxanthin · ligand · 2 copies · chains 1, 7, 8
- CL0 · Chlorophyll A isomer · ligand · chains A, B
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · chains A, L
- 3PH · 1,2-diacyl-glycerol-3-sn-phosphate · ligand · chains A, J, 7
- LPX · (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate · ligand · chains B, F
- 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 · chains A, F
- ECH · beta,beta-caroten-4-one · ligand · chains B, M
- QTB · (3~{E},5~{E},7~{E})-6-methyl-8-[(6~{R})-2,2,6-trimethylcyclohexyl]octa-3,5,7-trien-2-one · ligand · chains a
- 13X · benzene-1,3,5-triol · ligand · chains 6
- 4RF · Tripalmitoylglycerol · ligand · chains F, J, 7
- P5S · O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy) propyl]oxy}(hydroxy)phosphoryl]-L-serine · ligand · chains 8
- LAP · [2-((1-oxododecanoxy-(2-hydroxy-3-propanyl))-phosphonate-oxy)-ethyl]-trimethylammonium · ligand · chains F, 1, 8
- LMT · Dodecyl-beta-D-maltoside · additive · 4 copies · chains 3, 7, G, 1, M, I, 2
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 | 1002 | 0.80 | 0.81 | 83 | CLA |
| 2 | 983 | 0.79 | 0.81 | 74 | CLA, DGD |
| 3 | 1129 | 0.78 | 0.80 | 113 | CLA, SQD, LHG |
| 4 | 450 | 0.78 | 0.85 | 50 | CL0, CLA |
| 5 | 860 | 0.74 | 0.78 | 110 | CLA |
Interfaces
57 interfaces between chains.
- A–B · 3558 Ų buried · 43 hydrogen bonds · protein-protein
- H–L · 1962 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1591 Ų buried · 23 hydrogen bonds · protein-protein
- B–G · 1461 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 1152 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6ZZX · Structure of low-light grown Chlorella ohadii Photosystem I · 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
- Every structure of UniProt W8SY74
- Every structure of UniProt W8SUA3
- Every structure of UniProt W8SKM2
- Every structure of UniProt A0A2P6TKF8
- Every structure of UniProt A0A2P6U4S6
- Every structure of UniProt A0A2P6TPV8
- Every structure of UniProt A0A2P6TZI8
- Every structure of UniProt A0A2P6TPU7
- Every structure of UniProt W8SUD1
- Every structure of UniProt A0A2P6U0J1
- Every structure of UniProt A0A2P6TC44
- Every structure of UniProt W8SU98
- Every structure of UniProt W8SIP9
- Every structure of UniProt A0A2P6THB2
- Every structure of UniProt A0A2P6TT36
- Every structure of UniProt A0A2P6TMT4
- Every structure of UniProt A0A2P6U4K1
- Every structure of UniProt A0A2P6TPR7
- Every structure of UniProt A0A2P6TZ50
- Every structure of UniProt A0A2P6TMX4
- Every structure of UniProt A0A2P6TMI2
- Elsewhere: RCSB PDB 6ZZX · PDBe 6ZZX · UniProt W8SY74 · UniProt W8SUA3 · UniProt W8SKM2 · UniProt A0A2P6TKF8 · UniProt A0A2P6U4S6 · UniProt A0A2P6TPV8 · UniProt A0A2P6TZI8 · UniProt A0A2P6TPU7 · UniProt W8SUD1 · UniProt A0A2P6U0J1 · UniProt A0A2P6TC44 · UniProt W8SU98 · UniProt W8SIP9 · UniProt A0A2P6THB2 · UniProt A0A2P6TT36 · UniProt A0A2P6TMT4 · UniProt A0A2P6U4K1 · UniProt A0A2P6TPR7 · UniProt A0A2P6TZ50 · UniProt A0A2P6TMX4 · UniProt A0A2P6TMI2
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