MolNFT v1 · #182920 · protein
High-resolution structure of photosystem II from the mesophilic cyanobacterium, synechocystis sp. pcc 6803
7N8O · Photosystem II protein D1 2: “High-resolution structure of photosystem II from the mesophilic cyanobacterium, synechocystis sp. pcc 6803”. Electron microscopy, 15 ligands (CLA, BCR, SQD), 20 pockets (best druggability 0.89). MolNFT…
- PDB
- 7N8O
- Type
- protein
- Length
- 5,544 residues
- Chains
- 42
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosystem II protein D1 2; Photosystem II CP47 reaction center protein; Photosystem II…
- EC
- 1.10.3.9
- UniProt
- P16033, P05429, P09193, P09192, P09190, P09191, P14835, Q54697, P73070, P15819, Q55354, P72701, P10549, P73048, P73676, P74787, Q55332, Q55013, P72575, Q55438, P73528
- Ligands
- CLA, BCR, SQD, LHG, LMG, DGD, PHO, PL9, HEM, OEX, BCT, RRX, CA, FE2, CL
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 21 distinct chains · 55% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a | Photosystem II protein D1 2 (EC 1.10.3.9) | protein | 334 | 60% helix, 4% strand | P16033 |
| B, b | Photosystem II CP47 reaction center protein | protein | 503 | 50% helix, 11% strand | P05429 |
| C, c | Photosystem II CP43 reaction center protein | protein | 450 | 55% helix, 5% strand | P09193 |
| D, d | Photosystem II D2 protein (EC 1.10.3.9) | protein | 341 | 65% helix, 4% strand | P09192 |
| E, e | Cytochrome B559 subunit alpha | protein | 78 | 54% helix, 1% strand | P09190 |
| F, f | Cytochrome B559 subunit beta | protein | 35 | 66% helix, 0% strand | P09191 |
| H, h | Photosystem II reaction center protein H | protein | 63 | 52% helix, 3% strand | P14835 |
| I, i | Photosystem II reaction center protein I | protein | 36 | 72% helix, 0% strand | Q54697 |
| J, j | Photosystem II reaction center protein J | protein | 39 | 62% helix, 3% strand | P73070 |
| K, k | Photosystem II reaction center protein K | protein | 37 | 68% helix, 0% strand | P15819 |
| L, l | Photosystem II reaction center protein L | protein | 39 | 59% helix, 3% strand | Q55354 |
| M, m | Photosystem II reaction center protein M | protein | 31 | 71% helix, 0% strand | P72701 |
| O, o | Photosystem II manganese-stabilizing polypeptide | protein | 243 | 7% helix, 45% strand | P10549 |
| Q, q | SLL1638 protein | protein | 119 | 78% helix, 0% strand | P73048 |
| R, r | Photosystem II protein Y | protein | 34 | 91% helix, 0% strand | P73676 |
| T, t | Photosystem II reaction center protein T | protein | 30 | 70% helix, 0% strand | P74787 |
| U, u | Photosystem II 12 kda extrinsic protein | protein | 95 | 48% helix, 4% strand | Q55332 |
| V, v | Cytochrome C-550 | protein | 135 | 42% helix, 6% strand | Q55013 |
| X, x | Photosystem II reaction center X protein | protein | 38 | 82% helix, 0% strand | P72575 |
| Y, y | Photosystem II reaction center protein YCF12 | protein | 32 | 81% helix, 0% strand | Q55438 |
| Z, z | Photosystem II reaction center protein Z | protein | 60 | 88% helix, 0% strand | P73528 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 70 copies · chains A, D, T, F, I, B, H, L, M, t, C, K, Y, Z, X, a, d, f, i, b, h, l, m, c, k, y, z, x
- BCR · Beta-carotene · ligand · 18 copies · chains A, I, B, M, t, L, C, D, F, J, K, Y, Z, a, i, T, b, m, l, c, d, f, j, k, y, z
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 14 copies · chains A, C, T, b, h, l, B, L, m, t, D, K, E, F, R, X, H, a, c, M, d, k, e, f, r, x
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 14 copies · chains B, A, D, L, M, T, C, E, F, Z, b, a, d, l, m, t, c, e, f, z
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 12 copies · chains A, C, I, O, b, B, D, L, M, J, K, Y, F, a, c, i, o, d, l, m, j, k, y, f
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 8 copies · chains A, C, J, D, V, B, H, a, c, j, d, v, b, h
- PHO · Pheophytin A · ligand · 4 copies · chains A, D, a, d
- PL9 · 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2, 6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone · ligand · 4 copies · chains A, D, F, X, L, T, a, d, f, x, l, t
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains E, F, R, C, V, e, f, r, c, v
- OEX · Ca-MN4-O5 cluster · ligand · 2 copies · chains A, C, a, c
- BCT · Bicarbonate ion · ligand · 2 copies · chains A, D, a, d
- RRX · (3R)-beta,beta-caroten-3-ol · ligand · 2 copies · chains H, X, h, x
- CA · Calcium ion · metal · 6 copies · chains C, K, Y, B, U, V, c, k, y, b, u, v
- FE2 · Fe (II) ion · metal · 2 copies · chains A, D, a, d
- CL · Chloride ion · ion · 4 copies · chains A, D, C, a, d, c
- LMT · Dodecyl-beta-D-maltoside · additive · 62 copies · chains A, D, O, T, b, I, B, H, M, t, C, Z, E, X, F, R, J, K, L, l, m, Y, a, d, o, i, h, c, z, e, x, f, r, j, k, y
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 | 958 | 0.89 | 0.91 | 104 | HEM |
| 2 | 1022 | 0.87 | 0.88 | 82 | CLA, BCR |
| 3 | 1109 | 0.86 | 0.87 | 114 | HEM |
| 4 | 1189 | 0.86 | 0.86 | 85 | CLA, BCR |
| 5 | 1147 | 0.84 | 0.85 | 124 | DGD |
Interfaces
147 interfaces between chains.
- a–d · 5451 Ų buried · 65 hydrogen bonds · protein-protein
- A–D · 5443 Ų buried · 65 hydrogen bonds · protein-protein
- a–c · 3281 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 3271 Ų buried · 39 hydrogen bonds · protein-protein
- B–D · 2997 Ų buried · 49 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (formylation).
Compared structures
- 7N8O · High-resolution structure of photosystem II from the mesophilic cyanobacterium… · the same entry in another collection · chain F against F, 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 P16033
- Every structure of UniProt P05429
- Every structure of UniProt P09193
- Every structure of UniProt P09192
- Every structure of UniProt P09190
- Every structure of UniProt P09191
- Every structure of UniProt P14835
- Every structure of UniProt Q54697
- Every structure of UniProt P73070
- Every structure of UniProt P15819
- Every structure of UniProt Q55354
- Every structure of UniProt P72701
- Every structure of UniProt P10549
- Every structure of UniProt P73048
- Every structure of UniProt P73676
- Every structure of UniProt P74787
- Every structure of UniProt Q55332
- Every structure of UniProt Q55013
- Every structure of UniProt P72575
- Every structure of UniProt Q55438
- Every structure of UniProt P73528
- Elsewhere: RCSB PDB 7N8O · PDBe 7N8O · UniProt P16033 · UniProt P05429 · UniProt P09193 · UniProt P09192 · UniProt P09190 · UniProt P09191 · UniProt P14835 · UniProt Q54697 · UniProt P73070 · UniProt P15819 · UniProt Q55354 · UniProt P72701 · UniProt P10549 · UniProt P73048 · UniProt P73676 · UniProt P74787 · UniProt Q55332 · UniProt Q55013 · UniProt P72575 · UniProt Q55438 · UniProt P73528
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