MolNFT v1 · #154413 · protein
Cryo-EM structure of the C2S2-type psii-lhcii supercomplex from chlamydomonas reihardtii
6KAC · Photosystem II protein D1: “Cryo-EM structure of the C2S2-type psii-lhcii supercomplex from chlamydomonas reihardtii”. Electron microscopy, 18 ligands (CLA, CHL, BCR), 20 pockets (best druggability 0.87). MolNFT v1 #154413 on…
- PDB
- 6KAC
- Type
- protein
- Length
- 7,858 residues
- Chains
- 56
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosystem II protein D1; Photosystem II CP47 reaction center protein; Photosystem II…
- EC
- 1.10.3.9
- UniProt
- P07753, P37255, P10898, P06007, P48268, Q08363, P22666, P59763, O19930, P18263, P32974, P92277, P12853, P11471, P12852, P37256, Q9SPI9, A8I846, P92276, Q93WL4, Q93WE0, Q93WD2, Q9FEK6, Q93VE0, A8I5A0
- Ligands
- CLA, CHL, BCR, LHG, LUT, LMG, DGD, NEX, XAT, LMU, PHO, SQD, OEX, BCT, PL9, HEM…
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 28 distinct chains · 48% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a | Photosystem II protein D1 (EC 1.10.3.9) | protein | 336 | 59% helix, 4% strand | P07753 |
| B, b | Photosystem II CP47 reaction center protein | protein | 490 | 49% helix, 12% strand | P37255 |
| V, v | Photosystem II reaction center protein YCF12 | protein | 32 | 72% helix, 0% strand | — |
| C, c | Photosystem II CP43 reaction center protein | protein | 449 | 53% helix, 5% strand | P10898 |
| D, d | Photosystem II D2 protein (EC 1.10.3.9) | protein | 348 | 57% helix, 3% strand | P06007 |
| E, e | Cytochrome B559 subunit alpha | protein | 76 | 42% helix, 0% strand | P48268 |
| F, f | Cytochrome B559 subunit beta | protein | 31 | 74% helix, 3% strand | Q08363 |
| H, h | Photosystem II reaction center protein H | protein | 68 | 51% helix, 6% strand | P22666 |
| I, i | Photosystem II reaction center protein I | protein | 35 | 66% helix, 0% strand | P59763 |
| J, j | Photosystem II reaction center protein J | protein | 36 | 58% helix, 0% strand | O19930 |
| K, k | Photosystem II reaction center protein K | protein | 37 | 68% helix, 0% strand | P18263 |
| L, l | Photosystem II reaction center protein L | protein | 35 | 63% helix, 3% strand | P32974 |
| M, m | Photosystem II reaction center protein M | protein | 30 | 87% helix, 0% strand | P92277 |
| O, o | Oxygen-evolving enhancer protein 1, chloroplastic | protein | 240 | 5% helix, 44% strand | P12853 |
| P, p | Oxygen-evolving enhancer protein 2, chloroplastic | protein | 188 | 18% helix, 37% strand | P11471 |
| Q, q | Oxygen-evolving enhancer protein 3, chloroplastic | protein | 148 | 58% helix, 3% strand | P12852 |
| T, t | Photosystem II reaction center protein T | protein | 30 | 70% helix, 0% strand | P37256 |
| W, w | Photosystem II reaction center W protein, chloroplastic | protein | 56 | 48% helix, 4% strand | Q9SPI9 |
| X, x | 4.1 kda photosystem II subunit | protein | 35 | 86% helix, 0% strand | A8I846 |
| Z, z | Photosystem II reaction center protein Z | protein | 61 | 85% helix, 0% strand | P92276 |
| N, n | Chlorophyll a-B binding protein, chloroplastic | protein | 219 | 45% helix, 2% strand | Q93WL4 |
| G, g | Chlorophyll a-B binding protein, chloroplastic | protein | 219 | 49% helix, 2% strand | Q93WE0 |
| R, r | Chlorophyll a-B binding protein CP29 | protein | 183 | 43% helix, 7% strand | Q93WD2 |
| S, s | Chlorophyll a-B binding protein, chloroplastic | protein | 252 | 42% helix, 3% strand | Q9FEK6 |
| Y, y | Chlorophyll a-B binding protein, chloroplastic | protein | 221 | 49% helix, 1% strand | Q93VE0 |
| U, u | Predicted protein | protein | 24 | 33% helix, 0% strand | A8I5A0 |
| 1, 0 | 10 kda photosystem II polypeptide psbr (potential) | protein | 25 | 76% helix, 0% strand | — |
| 4, 3 | Unindentified stromal protein (usp) | protein | 25 | 16% helix, 0% strand | — |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 148 copies · chains A, D, T, L, I, W, B, H, M, m, t, C, S, K, V, Z, X, N, Y, G, R, r, a, d, l, i, w, b, h, c, s, k, v, z, x, n, y, g
- CHL · Chlorophyll B · ligand · 50 copies · chains N, G, S, Y, R, B, r, n, g, s, y, b
- BCR · Beta-carotene · ligand · 20 copies · chains A, I, B, M, t, C, K, Z, S, V, J, D, F, H, X, a, i, T, b, m, c, k, z, s, v, j, d, f, h, x
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 18 copies · chains C, S, A, B, D, L, T, M, N, G, Y, c, s, a, b, d, l, t, m, n, g, y
- LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 16 copies · chains N, G, S, Y, n, g, s, y
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 10 copies · chains A, C, I, W, B, D, L, M, V, J, K, F, E, H, a, c, i, w, b, d, l, m, v, j, k, f, e, h
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 10 copies · chains A, C, J, D, W, Y, I, a, c, j, d, w, y, i
- NEX · (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R, 6R)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13, 15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol · ligand · 10 copies · chains N, S, G, R, y, Y, r, n, s, g
- XAT · (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-tetrahydro-beta,beta-carotene-3,3'-diol · ligand · 8 copies · chains N, Y, G, R, n, y, g, r
- LMU · Dodecyl-alpha-D-maltoside · ligand · 6 copies · chains C, K, Z, S, c, k, z, s
- PHO · Pheophytin A · ligand · 4 copies · chains A, D, a, d
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 4 copies · chains A, C, D, K, B, l, m, t, a, c, d, k, L, M, T, b
- OEX · Ca-MN4-O5 cluster · ligand · 2 copies · chains A, C, a, c
- BCT · Bicarbonate ion · ligand · 2 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 · 2 copies · chains A, D, L, T, a, d, l, t
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains E, F, e, f
- 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 | 1004 | 0.87 | 0.88 | 79 | CLA, BCR |
| 2 | 993 | 0.87 | 0.87 | 84 | CLA, BCR |
| 3 | 963 | 0.85 | 0.86 | 98 | CLA, LMG |
| 4 | 979 | 0.85 | 0.86 | 109 | CLA, LMG |
| 5 | 1002 | 0.85 | 0.85 | 105 | CLA, DGD |
Interfaces
174 interfaces between chains.
- a–d · 5483 Ų buried · 79 hydrogen bonds · protein-protein
- A–D · 5478 Ų buried · 77 hydrogen bonds · protein-protein
- a–c · 3345 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 3344 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 2820 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 6KAC · Cryo-EM structure of the C2S2-type PSII-LHCII supercomplex from Chlamydomonas reihardtii · 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 P07753
- Every structure of UniProt P37255
- Every structure of UniProt P10898
- Every structure of UniProt P06007
- Every structure of UniProt P48268
- Every structure of UniProt Q08363
- Every structure of UniProt P22666
- Every structure of UniProt P59763
- Every structure of UniProt O19930
- Every structure of UniProt P18263
- Every structure of UniProt P32974
- Every structure of UniProt P92277
- Every structure of UniProt P12853
- Every structure of UniProt P11471
- Every structure of UniProt P12852
- Every structure of UniProt P37256
- Every structure of UniProt Q9SPI9
- Every structure of UniProt A8I846
- Every structure of UniProt P92276
- Every structure of UniProt Q93WL4
- Every structure of UniProt Q93WE0
- Every structure of UniProt Q93WD2
- Every structure of UniProt Q9FEK6
- Every structure of UniProt Q93VE0
- Every structure of UniProt A8I5A0
- Elsewhere: RCSB PDB 6KAC · PDBe 6KAC · UniProt P07753 · UniProt P37255 · UniProt P10898 · UniProt P06007 · UniProt P48268 · UniProt Q08363 · UniProt P22666 · UniProt P59763 · UniProt O19930 · UniProt P18263 · UniProt P32974 · UniProt P92277 · UniProt P12853 · UniProt P11471 · UniProt P12852 · UniProt P37256 · UniProt Q9SPI9 · UniProt A8I846 · UniProt P92276 · UniProt Q93WL4 · UniProt Q93WE0 · UniProt Q93WD2 · UniProt Q9FEK6 · UniProt Q93VE0 · UniProt A8I5A0
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