Research workbench
Rt xfel structure of photosystem II in the dark state at 3.0 a resolution
Analyse Rt xfel structure of photosystem II in the dark state at 3.0 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KAF
- Type
- protein
- Length
- 5,319 residues
- Chains
- 40
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosystem II protein D1 1; Photosystem II CP47 reaction center 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, Q8DKM3
- Ligands
- CLA, BCR, UNL, LMG, LHG, SQD, DGD, PHO, PL9, OEX, BCT, HEM, HEC, FE2, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 21 distinct chains · 52% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a | Photosystem II protein D1 1 (EC 1.10.3.9) | protein | 334 | 61% helix, 4% strand | P0A444 |
| B, b | Photosystem II CP47 reaction center protein | protein | 504 | 47% helix, 11% strand | Q8DIQ1 |
| C, c | Photosystem II CP43 reaction center protein | protein | 451 | 58% helix, 5% strand | Q8DIF8 |
| D, d | Photosystem II D2 protein (EC 1.10.3.9) | protein | 341 | 58% helix, 4% strand | Q8CM25 |
| E | Cytochrome B559 subunit alpha | protein | 81 | 54% helix, 0% strand | Q8DIP0 |
| F, f | Cytochrome B559 subunit beta | protein | 34 | 68% helix, 0% strand | Q8DIN9 |
| H, h | Photosystem II reaction center protein H | protein | 63 | 49% helix, 3% strand | Q8DJ43 |
| I, i | Photosystem II reaction center protein I | protein | 36 | 69% helix, 0% strand | Q8DJZ6 |
| J, j | Photosystem II reaction center protein J | protein | 36 | 61% helix, 0% strand | P59087 |
| K, k | Photosystem II reaction center protein K | protein | 37 | 73% 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 | 33 | 73% helix, 3% strand | Q8DHA7 |
| O, o | Photosystem II manganese-stabilizing polypeptide | protein | 244 | 5% helix, 46% strand | P0A431 |
| T, t | Photosystem II reaction center protein T | protein | 30 | 70% helix, 0% strand | Q8DIQ0 |
| U, u | Photosystem II 12 kda extrinsic protein | protein | 97 | 48% helix, 4% strand | Q9F1L5 |
| V, v | Cytochrome C-550 | protein | 137 | 44% helix, 6% strand | P0A386 |
| Y, y | Photosystem II reaction center protein YCF12 | protein | 30 | 70% helix, 0% strand | Q8DJI1 |
| X, x | Photosystem II reaction center X protein | protein | 38 | 79% helix, 0% strand | Q9F1R6 |
| Z, z | Photosystem II reaction center protein Z | protein | 62 | 79% helix, 0% strand | Q8DHJ2 |
| R, r | Photosystem II protein Y | protein | 34 | 88% helix, 0% strand | Q8DKM3 |
| e | Cytochrome B559 subunit alpha | protein | 82 | 52% helix, 0% strand | Q8DIP0 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 70 copies · chains A, D, T, I, L, B, H, M, t, C, K, Y, Z, X, a, d, i, l, b, h, m, c, k, y, z, x
- BCR · Beta-carotene · ligand · 22 copies · chains A, I, B, M, t, a, C, K, Z, D, F, J, H, X, T, b, Y, i, m, c, k, z, d, f, j, h, x, y
- UNL · Unknown ligand · ligand · 17 copies · chains A, B, D, a, C, H, M, L, m, T, b, d, x, i, j, t, c, z
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 16 copies · chains A, C, I, T, b, B, D, L, M, H, a, t, J, K, Y, F, d, l, m, c, i, j, k, y, f, x
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 10 copies · chains A, B, D, L, M, C, E, F, T, a, b, d, l, m, c, e, t
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 9 copies · chains A, C, D, K, O, b, B, L, l, m, t, E, F, X, R, I, M, T, a, c, d, k, e, f, x, r
- 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
- OEX · Ca-MN4-O5 cluster · ligand · 2 copies · chains A, C, a, c
- BCT · Bicarbonate ion · ligand · 2 copies · chains A, D, a, d
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains E, F, R, e, f, r
- HEC · Heme C · ligand · 2 copies · chains C, V, c, 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
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 | 1032 | 0.87 | 0.88 | 79 | CLA, BCR |
| 2 | 1012 | 0.87 | 0.87 | 78 | CLA, BCR |
| 3 | 1048 | 0.85 | 0.86 | 83 | HEC |
| 4 | 1116 | 0.84 | 0.85 | 98 | HEC |
| 5 | 766 | 0.84 | 0.86 | 80 | LHG |
Interfaces
138 interfaces between chains.
- A–D · 5482 Ų buried · 62 hydrogen bonds · protein-protein
- a–d · 5467 Ų buried · 64 hydrogen bonds · protein-protein
- A–C · 3293 Ų buried · 39 hydrogen bonds · protein-protein
- a–c · 3253 Ų buried · 36 hydrogen bonds · protein-protein
- b–d · 3016 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified, 4 cofactor, 2 disulfide (formylation, heme c attachment, disulfide).
Compared structures
- 5KAF · RT XFEL structure of Photosystem II in the dark state at 3.0 A resolution · the same entry in another collection · chain K against K, 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
- Every structure of UniProt Q8DKM3
- Elsewhere: RCSB PDB 5KAF · PDBe 5KAF · 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 · UniProt Q8DKM3
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