MolNFT v1 · #134904 · protein
Room temperature xfel structure of the native, doubly-illuminated photosystem II complex
5TIS · Photosystem II protein D1 1: “Room temperature xfel structure of the native, doubly-illuminated photosystem II complex”. X-ray diffraction, 15 ligands (CLA, UNL, BCR), 20 pockets (best druggability 0.87). MolNFT v1 #134904 on…
- PDB
- 5TIS
- 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, UNL, BCR, LMG, SQD, LHG, DGD, PHO, PL9, OEX, BCT, HEM, HEC, FE2, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 24 distinct chains · 54% 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 | 60% helix, 4% strand | P0A444 |
| B, b | Photosystem II CP47 reaction center protein | protein | 504 | 48% helix, 10% 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 | 62% helix, 4% strand | Q8CM25 |
| E | Cytochrome B559 subunit alpha | protein | 81 | 57% helix, 0% strand | Q8DIP0 |
| F, f | Cytochrome B559 subunit beta | protein | 34 | 68% helix, 0% strand | Q8DIN9 |
| H | Photosystem II reaction center protein H | protein | 65 | 52% helix, 3% strand | Q8DJ43 |
| I | Photosystem II reaction center protein I | protein | 37 | 70% 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 | 78% 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, 0% strand | Q8DHA7 |
| O, o | Photosystem II manganese-stabilizing polypeptide | protein | 244 | 5% helix, 48% 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 | 47% helix, 4% strand | Q9F1L5 |
| V, v | Cytochrome C-550 | protein | 137 | 47% helix, 6% strand | P0A386 |
| Y | Photosystem II reaction center protein YCF12 | protein | 27 | 81% 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 | 82% helix, 0% strand | Q8DHJ2 |
| R, r | Photosystem II protein Y | protein | 34 | 85% helix, 0% strand | Q8DKM3 |
| e | Cytochrome B559 subunit alpha | protein | 82 | 52% helix, 0% strand | Q8DIP0 |
| h | Photosystem II reaction center protein H | protein | 63 | 51% helix, 3% strand | Q8DJ43 |
| i | Photosystem II reaction center protein I | protein | 36 | 69% helix, 0% strand | Q8DJZ6 |
| y | Photosystem II reaction center protein YCF12 | protein | 30 | 80% helix, 0% strand | Q8DJI1 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 70 copies · chains A, D, I, L, T, B, H, M, t, C, K, Y, Z, X, a, d, f, i, l, b, h, m, c, k, y, z, x
- UNL · Unknown ligand · ligand · 33 copies · chains A, D, b, B, M, m, t, C, K, X, E, H, I, J, Y, L, T, a, d, h, c, k, z, i, j, l, x
- BCR · Beta-carotene · ligand · 22 copies · chains A, I, B, M, t, C, K, Z, D, F, J, H, X, T, b, Y, a, i, m, c, k, z, j, y, d, f, h, x
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 14 copies · chains B, D, L, M, H, a, o, t, A, C, I, K, Y, F, J, c, i, b, h, k, y, d, f, j, x, l, m
- 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, T, b, B, L, l, m, t, H, a, E, F, X, R, M, c, d, j, k, O, e, f, x, r
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 10 copies · chains A, C, D, E, F, B, L, M, T, a, c, d, e, f, b, l, m, t
- 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, L, T, a, d, f, 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 | 1024 | 0.87 | 0.87 | 86 | CLA, BCR |
| 2 | 963 | 0.86 | 0.87 | 77 | CLA, BCR |
| 3 | 983 | 0.86 | 0.86 | 80 | HEC |
| 4 | 1027 | 0.85 | 0.86 | 84 | HEC |
| 5 | 1065 | 0.83 | 0.84 | 94 | LHG, PL9 |
Interfaces
137 interfaces between chains.
- A–D · 5435 Ų buried · 66 hydrogen bonds · protein-protein
- a–d · 5430 Ų buried · 62 hydrogen bonds · protein-protein
- A–C · 3256 Ų buried · 37 hydrogen bonds · protein-protein
- a–c · 3242 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 3003 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified, 4 cofactor, 2 disulfide (formylation, heme c attachment, disulfide).
Compared structures
- 5TIS · Room temperature XFEL structure of the native, doubly-illuminated photosystem II complex · 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
- Every structure of UniProt Q8DKM3
- Elsewhere: RCSB PDB 5TIS · PDBe 5TIS · 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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