Research workbench
Rt xfel structure of photosystem II in the dark state at 4.9 a resolution
Analyse Rt xfel structure of photosystem II in the dark state at 4.9 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TNH
- Type
- protein
- Length
- 5,270 residues
- Chains
- 40
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosystem Q(B) protein 1; Photosystem II core light harvesting protein; Photosystem II…
- EC
- 1.10.3.9
- UniProt
- P0A444, Q8DIQ1, Q8DIF8, Q8CM25, Q8DIP0, Q8DIN9, Q8DJ43, Q8DJZ6, P59087, Q9F1K9, Q8DIN8, Q8DHA7, P0A431, Q8DIQ0, Q9F1L5, P0A386, Q8DJI1, Q9F1R6, Q8DHJ2
- Ligands
- CLA, BCR, LMG, DGD, SQD, PL9, LHG, PHO, HEM, OEX, BCT, CA, FE2, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 20 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a | Photosystem Q(B) protein 1 (EC 1.10.3.9) | protein | 335 | 60% helix, 4% strand | P0A444 |
| B, b | Photosystem II core light harvesting protein | protein | 490 | 49% helix, 11% strand | Q8DIQ1 |
| C, c | Photosystem II CP43 protein | protein | 447 | 56% helix, 5% strand | Q8DIF8 |
| D, d | Photosystem II D2 protein (EC 1.10.3.9) | protein | 340 | 63% helix, 3% strand | Q8CM25 |
| E, e | Cytochrome B559 subunit alpha | protein | 82 | 54% helix, 0% strand | Q8DIP0 |
| F, f | Cytochrome B559 subunit beta | protein | 35 | 66% helix, 0% strand | Q8DIN9 |
| H, h | Photosystem II reaction center protein H | protein | 65 | 43% helix, 5% strand | Q8DJ43 |
| I, i | Photosystem II reaction center protein I | protein | 35 | 66% helix, 0% strand | Q8DJZ6 |
| J, j | Photosystem II reaction center protein J | protein | 34 | 65% helix, 0% strand | P59087 |
| K, k | Photosystem II reaction center protein K | protein | 37 | 70% helix, 0% strand | Q9F1K9 |
| L, l | Photosystem II reaction center protein L | protein | 37 | 62% helix, 3% strand | Q8DIN8 |
| M, m | Photosystem II reaction center protein M | protein | 34 | 71% helix, 0% strand | Q8DHA7 |
| O, o | Photosystem II manganese-stabilizing polypeptide | protein | 243 | 4% helix, 46% strand | P0A431 |
| T, t | Photosystem II reaction center protein T | protein | 32 | 66% helix, 0% strand | Q8DIQ0 |
| U, u | Photosystem II 12 kda extrinsic protein | protein | 97 | 48% helix, 6% strand | Q9F1L5 |
| V, v | Cytochrome C-550 | protein | 137 | 47% helix, 6% strand | P0A386 |
| y, g | Photosystem II reaction center protein YCF12 | protein | 28 | 71% helix, 0% strand | Q8DJI1 |
| X, x | Photosystem II reaction center X protein | protein | 37 | 76% helix, 0% strand | Q9F1R6 |
| Y, G | Photosystem II reaction center protein Y | protein | 28 | 75% helix, 0% strand | — |
| Z, z | Photosystem II reaction center protein Z | protein | 62 | 85% helix, 0% strand | Q8DHJ2 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 70 copies · chains A, D, T, L, F, I, B, H, M, m, t, C, K, y, Z, X, a, d, l, i, b, h, c, k, g, z, x
- BCR · Beta-carotene · ligand · 24 copies · chains A, I, B, M, t, a, C, K, Z, D, F, J, H, X, y, i, T, b, m, c, k, z, d, f, j, g, h, x
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 22 copies · chains A, B, D, L, M, O, b, C, Z, J, K, y, T, F, E, I, l, m, a, d, o, c, z, j, k, g, t, f, e, i
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 14 copies · chains A, C, I, O, B, D, H, a, J, V, E, F, c, i, o, b, d, h, j, v, e, f
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 10 copies · chains A, C, D, K, I, T, b, B, H, X, L, l, m, t, E, F, a, i, c, d, k, M, h, x, e, f
- 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 · 6 copies · chains A, D, F, L, T, J, a, d, f, l, t, j
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 4 copies · chains A, C, D, K, a, c, d, k
- PHO · Pheophytin A · ligand · 4 copies · chains A, D, a, d
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains E, F, Y, C, V, e, f, G, 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
- CA · Calcium ion · metal · 4 copies · chains C, K, O, c, k, o
- FE2 · Fe (II) ion · metal · 2 copies · chains A, D, a, d
- CL · Chloride ion · ion · 2 copies · chains A, D, a, d
- LMT · Dodecyl-beta-D-maltoside · additive · 14 copies · chains B, D, H, a, i, o, t, X, I, M, T, b, m, A, O, d, h, x
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 | 939 | 0.87 | 0.87 | 75 | CLA, BCR |
| 2 | 931 | 0.86 | 0.87 | 78 | CLA, BCR |
| 3 | 1050 | 0.85 | 0.86 | 97 | HEM |
| 4 | 1104 | 0.84 | 0.85 | 102 | HEM |
| 5 | 813 | 0.84 | 0.86 | 91 | LMG |
Interfaces
135 interfaces between chains.
- a–d · 5536 Ų buried · 62 hydrogen bonds · protein-protein
- A–D · 5533 Ų buried · 62 hydrogen bonds · protein-protein
- a–c · 3297 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 3290 Ų buried · 43 hydrogen bonds · protein-protein
- B–D · 2677 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4TNH · RT XFEL structure of Photosystem II in the dark state at 4.9 A resolution · the same entry in another collection · chain L against L, 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 P0A444
- Every structure of UniProt Q8DIQ1
- Every structure of UniProt Q8DIF8
- Every structure of UniProt Q8CM25
- Every structure of UniProt Q8DIP0
- Every structure of UniProt Q8DIN9
- Every structure of UniProt Q8DJ43
- Every structure of UniProt Q8DJZ6
- Every structure of UniProt P59087
- Every structure of UniProt Q9F1K9
- Every structure of UniProt Q8DIN8
- Every structure of UniProt Q8DHA7
- Every structure of UniProt P0A431
- Every structure of UniProt Q8DIQ0
- Every structure of UniProt Q9F1L5
- Every structure of UniProt P0A386
- Every structure of UniProt Q8DJI1
- Every structure of UniProt Q9F1R6
- Every structure of UniProt Q8DHJ2
- Elsewhere: RCSB PDB 4TNH · PDBe 4TNH · UniProt P0A444 · UniProt Q8DIQ1 · UniProt Q8DIF8 · UniProt Q8CM25 · UniProt Q8DIP0 · UniProt Q8DIN9 · UniProt Q8DJ43 · UniProt Q8DJZ6 · UniProt P59087 · UniProt Q9F1K9 · UniProt Q8DIN8 · UniProt Q8DHA7 · UniProt P0A431 · UniProt Q8DIQ0 · UniProt Q9F1L5 · UniProt P0A386 · UniProt Q8DJI1 · UniProt Q9F1R6 · UniProt Q8DHJ2
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