Research workbench
Structure of synechocystis photosystem I trimer at 2.5A resolution
Analyse Structure of synechocystis photosystem I trimer at 2.5A resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OY0
- Type
- protein
- Length
- 6,771 residues
- Chains
- 33
- Method
- x-ray diffraction
- 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
- P29254, P29255, P32422, P19569, P12975, P29256, Q55330, Q55329, P74564, P37277, P72986
- Ligands
- CLA, BCR, LHG, LMG, SF4, ECH, SQD, PQN, ZEX, 45D, EQ3, DGD, CA, MG, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 20 distinct chains · 55% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a | Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 751 | 61% helix, 5% strand | P29254 |
| B, 2 | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 731 | 60% helix, 2% strand | P29255 |
| C, 3 | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 16% helix, 20% strand | P32422 |
| D, d | Photosystem I reaction center subunit II | protein | 141 | 18% helix, 27% strand | P19569 |
| E, 5 | Photosystem I reaction center subunit IV | protein | 69 | 4% helix, 33% strand | P12975 |
| F, f, 6 | Photosystem I reaction center subunit III | protein | 143 | 56% helix, 6% strand | P29256 |
| I, i | Photosystem I reaction center subunit VIII | protein | 40 | 65% helix, 0% strand | Q55330 |
| J, j, 7 | Photosystem I reaction center subunit IX | protein | 40 | 73% helix, 3% strand | Q55329 |
| K | Photosystem I reaction center subunit psak 2 | protein | 80 | 49% helix, 0% strand | P74564 |
| L, l | Photosystem I reaction center subunit XI | protein | 157 | 66% helix, 4% strand | P37277 |
| M, m, 9 | Photosystem I reaction center subunit XII | protein | 31 | 81% helix, 0% strand | P72986 |
| b | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 729 | 61% helix, 3% strand | P29255 |
| c | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 81 | 16% helix, 27% strand | P32422 |
| e | Photosystem I reaction center subunit IV | protein | 68 | 4% helix, 34% strand | P12975 |
| k | Photosystem I reaction center subunit psak 2 | protein | 78 | 53% helix, 0% strand | P74564 |
| 1 | Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 744 | 61% helix, 5% strand | P29254 |
| 4 | Photosystem I reaction center subunit II | protein | 140 | 17% helix, 26% strand | P19569 |
| h | Photosystem I reaction center subunit VIII | protein | 38 | 68% helix, 0% strand | Q55330 |
| 8 | Photosystem I reaction center subunit psak 2 | protein | 79 | 57% helix, 0% strand | P74564 |
| 0 | Photosystem I reaction center subunit XI | protein | 154 | 65% helix, 5% strand | P37277 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 285 copies · chains A, B, J, K, L, I, b, F, D, m, M, 0, i, l, a, j, k, f, 2, 9, h, 1, 7, 8, 6
- BCR · Beta-carotene · ligand · 58 copies · chains A, K, J, B, F, I, L, l, a, k, f, j, b, i, 0, 1, 8, 7, 2, 6, h, 9
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 27 copies · chains A, E, b, m, L, i, B, F, M, a, e, 2, 9, l, h, 0, 1, 5, 6, I
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 16 copies · chains A, L, m, K, B, b, a, l, 9, 1, 0, M, 2, I
- SF4 · Iron/sulfur cluster · ligand · 9 copies · chains A, B, C, a, b, c, 1, 2, 3
- ECH · beta,beta-caroten-4-one · ligand · 7 copies · chains B, I, M, a, b, i, l, m, 2
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 7 copies · chains B, A, F, L, i, b, m, a, f, M, 1, 0
- PQN · Phylloquinone · ligand · 6 copies · chains A, J, B, a, j, b, 1, 7, 2
- ZEX · (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol · ligand · 4 copies · chains A, B, F, J, b, f, j, 2, 6, 7
- 45D · beta,beta-carotene-4,4'-dione · ligand · 2 copies · chains A, B, 2, h, 0
- EQ3 · (3'R)-3'-hydroxy-beta,beta-caroten-4-one · ligand · chains B, I, L
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · chains L, m
- CA · Calcium ion · metal · 6 copies · chains B, L, 0, b, a, l, 2, 1
- MG · Magnesium ion · metal · 2 copies · chains B, b
- CL · Chloride ion · ion · 3 copies · chains A, B, a, b, 1, 2
- LMT · Dodecyl-beta-D-maltoside · additive · 5 copies · chains F, J, L, i, l, h, 1, I, M, 0
- ACT · Acetate ion · additive · 4 copies · chains A, B, D, M
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 | 1138 | 0.86 | 0.86 | 99 | CLA |
| 2 | 813 | 0.84 | 0.86 | 87 | CLA |
| 3 | 805 | 0.84 | 0.86 | 98 | CLA |
| 4 | 780 | 0.83 | 0.85 | 65 | BCR |
| 5 | 1023 | 0.81 | 0.82 | 84 | CLA, LMG |
Interfaces
88 interfaces between chains.
- a–b · 3530 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 3526 Ų buried · 47 hydrogen bonds · protein-protein
- 1–2 · 3506 Ų buried · 40 hydrogen bonds · protein-protein
- 3–4 · 1595 Ų buried · 26 hydrogen bonds · protein-protein
- c–d · 1579 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 3 disulfide (covalent ligand, disulfide).
Compared structures
- 5OY0 · Structure of synechocystis photosystem I trimer at 2.5A resolution · 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 P29254
- Every structure of UniProt P29255
- Every structure of UniProt P32422
- Every structure of UniProt P19569
- Every structure of UniProt P12975
- Every structure of UniProt P29256
- Every structure of UniProt Q55330
- Every structure of UniProt Q55329
- Every structure of UniProt P74564
- Every structure of UniProt P37277
- Every structure of UniProt P72986
- Elsewhere: RCSB PDB 5OY0 · PDBe 5OY0 · UniProt P29254 · UniProt P29255 · UniProt P32422 · UniProt P19569 · UniProt P12975 · UniProt P29256 · UniProt Q55330 · UniProt Q55329 · UniProt P74564 · UniProt P37277 · UniProt P72986
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