Research workbench
Crystal structure of photosystem II from thermosynechococcus elongatus
Analyse Crystal structure of photosystem II from thermosynechococcus elongatus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AXT
- Type
- protein
- Length
- 5,286 residues
- Chains
- 36
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosystem Q(B) protein; CP47 protein; Photosystem II CP43 protein; Photosystem II…
- UniProt
- P0A445, Q8DIP0, Q8DIN9, Q8DJ43, Q8DJZ6, P59087, Q9F1K9, Q8DIN8, Q8DHA7, P0A431, Q8DIQ0, Q9F1L5, P0A386, Q8DHJ2
- Ligands
- CLA, UNK, BCR, MGE, DGD, SQD, PHO, PQ9, HEM, OEC, LHG, BCT, FE2, CA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 18 distinct chains · 51% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a | Photosystem Q(B) protein | protein | 335 | 57% helix, 4% strand | P0A445 |
| B, b | CP47 protein | protein | 488 | 47% helix, 10% strand | — |
| C, c | Photosystem II CP43 protein | protein | 447 | 53% helix, 3% strand | — |
| D, d | Photosystem II reaction center D2 protein | protein | 340 | 58% helix, 3% strand | — |
| E, e | Cytochrome B559 alpha subunit | protein | 82 | 55% helix, 0% strand | Q8DIP0 |
| F, f | Cytochrome B559 beta subunit | protein | 35 | 66% helix, 0% strand | Q8DIN9 |
| H, h | Photosystem II reaction center H protein | protein | 64 | 44% helix, 0% strand | Q8DJ43 |
| I, i | Photosystem II reaction center I protein | protein | 35 | 63% helix, 0% strand | Q8DJZ6 |
| J, j | Photosystem II reaction center J protein | protein | 34 | 65% helix, 0% strand | P59087 |
| K, k | Photosystem II reaction center protein K | protein | 37 | 78% helix, 0% strand | Q9F1K9 |
| L, l | Photosystem II reaction center L protein | protein | 37 | 62% helix, 3% strand | Q8DIN8 |
| M, m | Photosystem II reaction center M protein | protein | 36 | 75% helix, 0% strand | Q8DHA7 |
| O, o | Photosystem II manganese-stabilizing polypeptide | protein | 242 | 5% helix, 46% strand | P0A431 |
| T, t | Photosystem II reaction center T protein | protein | 30 | 70% helix, 0% strand | Q8DIQ0 |
| U, u | Photosystem II 12 kda extrinsic protein | protein | 98 | 44% helix, 6% strand | Q9F1L5 |
| V, v | Cytochrome C-550 | protein | 137 | 50% helix, 6% strand | P0A386 |
| X, x | Unassigned subunits | protein | 104 | 71% helix, 0% strand | — |
| Z, z | Photosystem II reaction center Z protein | protein | 62 | 87% helix, 0% strand | Q8DHJ2 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 70 copies · chains A, D, T, L, I, B, H, M, m, C, K, X, Z, a, d, t, l, i, b, h, c, k, x, z
- UNK · Unknown · ligand · 34 copies · chains A, D, L, T, M, m, C, K, J, X, B, H, F, b, I, a, d, l, t, c, k, j, x, h, f, i
- BCR · Beta-carotene · ligand · 22 copies · chains A, I, b, B, M, t, C, K, Z, D, F, J, H, X, T, a, i, m, c, k, z, d, f, j, h, x
- MGE · (1S)-2-(alpha-L-allopyranosyloxy)-1-[(tridecanoyloxy) methyl]ethyl palmitate · ligand · 12 copies · chains B, L, M, D, F, J, A, T, C, I, b, l, m, d, f, j, a, t, c, i
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 8 copies · chains A, C, J, D, V, B, H, a, c, j, d, v, b, h
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 6 copies · chains A, C, D, J, K, T, b, L, M, l, B, a, t, c, d, j, k, m
- PHO · Pheophytin A · ligand · 4 copies · chains A, D, a, d
- PQ9 · 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-heptamethyloctacosa-2,6,10,14,18,22,26-heptaenyl]-2,3-dimethylbenzo-1,4-quinone · ligand · 4 copies · chains A, D, a, d
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains E, F, X, C, V, e, f, x, c, v
- OEC · Oxygen evolving system · ligand · 2 copies · chains A, C, a, c
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 2 copies · chains A, C, D, a, c, d
- BCT · Bicarbonate ion · ligand · 2 copies · chains A, D, a, d
- FE2 · Fe (II) ion · metal · 2 copies · chains A, D, a, d
- CA · Calcium ion · metal · 2 copies · chains C, K, X, c, k, x
- LMT · Dodecyl-beta-D-maltoside · additive · 6 copies · chains A, D, O, b, B, M, m, t, T, a, d, o
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 | 1010 | 0.86 | 0.86 | 84 | HEM |
| 2 | 1022 | 0.85 | 0.86 | 85 | HEM |
| 3 | 1135 | 0.85 | 0.85 | 86 | CLA, BCR |
| 4 | 1146 | 0.85 | 0.85 | 82 | CLA, BCR |
| 5 | 231 | 0.83 | 0.95 | 35 | empty |
Interfaces
137 interfaces between chains.
- A–D · 5485 Ų buried · 69 hydrogen bonds · protein-protein
- a–d · 5483 Ų buried · 69 hydrogen bonds · protein-protein
- A–C · 3221 Ų buried · 39 hydrogen bonds · protein-protein
- a–c · 3216 Ų buried · 39 hydrogen bonds · protein-protein
- B–D · 2486 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2AXT · Crystal Structure of Photosystem II from Thermosynechococcus elongatus · the same entry in another collection · chain H against H, 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 P0A445
- 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 Q8DHJ2
- Elsewhere: RCSB PDB 2AXT · PDBe 2AXT · UniProt P0A445 · 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 Q8DHJ2
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