Research workbench
Architecture of the photosynthetic oxygen evolving center
Analyse Architecture of the photosynthetic oxygen evolving center in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S5L
- Type
- protein
- Length
- 5,130 residues
- Chains
- 38
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosystem Q(B) protein; Photosystem II core light harvesting protein; Photosystem II…
- UniProt
- P0A444, Q8DIQ1, Q8DIF8, Q8CM25, Q8DIP0, Q8DIN9, Q8DJ43, Q8DJZ6, P59087, Q9F1K9, Q8DIN8, Q8DHA7, P0A431, Q8DIQ0, Q9F1L5, P0A386, Q9F1R6, Q8DHJ2
- Ligands
- CLA, BCR, BCT, PHO, PL9, HEC, OEC, FE
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 19 distinct chains · 51% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a | Photosystem Q(B) protein | protein | 333 | 55% helix, 5% strand | P0A444 |
| B, b | Photosystem II core light harvesting protein | protein | 476 | 49% helix, 6% strand | Q8DIQ1 |
| C, c | Photosystem II CP43 protein | protein | 421 | 56% helix, 5% strand | Q8DIF8 |
| D, d | Photosystem II reaction center D2 protein | protein | 339 | 59% helix, 2% strand | Q8CM25 |
| E, e | Cytochrome B559 alpha subunit | protein | 76 | 62% helix, 0% strand | Q8DIP0 |
| F, f | Cytochrome B559 beta subunit | protein | 33 | 73% helix, 0% strand | Q8DIN9 |
| H, h | Photosystem II psbh protein | protein | 53 | 42% helix, 0% strand | Q8DJ43 |
| I, i | Photosystem II reaction center I protein | protein | 38 | 58% helix, 0% strand | Q8DJZ6 |
| J, j | Photosystem II reaction center J protein | protein | 38 | 66% helix, 0% strand | P59087 |
| K, k | Photosystem II reaction center protein K | protein | 37 | 81% helix, 0% strand | Q9F1K9 |
| L, l | Photosystem II reaction center L protein | protein | 37 | 62% helix, 0% strand | Q8DIN8 |
| M, m | Photosystem II reaction center M protein | protein | 30 | 80% helix, 0% strand | Q8DHA7 |
| O, o | Photosystem II manganese-stabilizing polypeptide | protein | 246 | 7% helix, 32% strand | P0A431 |
| T, t | Photosystem II psbt protein | protein | 31 | 61% helix, 0% strand | Q8DIQ0 |
| U, u | Photosystem II 12 kda extrinsic protein | protein | 105 | 42% helix, 4% strand | Q9F1L5 |
| V, v | Cytochrome C-550 | protein | 137 | 49% helix, 6% strand | P0A386 |
| X, x | Photosystem II psbx protein | protein | 40 | 73% helix, 0% strand | Q9F1R6 |
| N, n | Photosystem II psbn protein | protein | 37 | 78% helix, 0% strand | — |
| Z, z | Photosystem II reaction center Z protein | protein | 58 | 84% helix, 0% strand | Q8DHJ2 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 72 copies · chains A, D, T, L, C, I, B, H, M, J, K, Z, X, a, d, t, c, i, o, b, h, l, x, m, j, k, z
- BCR · Beta-carotene · ligand · 14 copies · chains B, M, C, K, Z, D, F, J, N, b, m, c, k, z, d, f, j, n
- BCT · Bicarbonate ion · ligand · 4 copies · chains A, C, D, a, c, d
- 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, E, D, L, T, a, e, d, l, t
- HEC · Heme C · ligand · 4 copies · chains E, F, C, V, e, f, c, v
- OEC · Oxygen evolving system · ligand · 2 copies · chains A, C, a, c
- FE · Fe (III) ion · metal · 2 copies · chains A, D, a, d
- LMT · Dodecyl-beta-D-maltoside · additive · 2 copies · chains B, D, E, H, b, d, e, h
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 | 791 | 0.87 | 0.89 | 80 | HEC |
| 2 | 983 | 0.86 | 0.87 | 90 | HEC |
| 3 | 975 | 0.84 | 0.85 | 75 | BCR |
| 4 | 924 | 0.84 | 0.85 | 100 | CLA, PL9 |
| 5 | 1163 | 0.83 | 0.83 | 88 | BCR |
Interfaces
127 interfaces between chains.
- A–D · 5434 Ų buried · 60 hydrogen bonds · protein-protein
- a–d · 5394 Ų buried · 62 hydrogen bonds · protein-protein
- a–c · 2888 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 2879 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 2469 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 2 disulfide, 1 covalent (heme c attachment, disulfide, covalent ligand).
Compared structures
- 1S5L · Architecture of the photosynthetic oxygen evolving center · 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 Q9F1R6
- Every structure of UniProt Q8DHJ2
- Elsewhere: RCSB PDB 1S5L · PDBe 1S5L · 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 Q9F1R6 · UniProt Q8DHJ2
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