MolNFT v1 · #168525 · protein
Cryo-EM structure of apo-photosystem II from synechocystis sp. pcc 6803
6WJ6 · Photosystem II protein D1 2: “Cryo-EM structure of apo-photosystem II from synechocystis sp. pcc 6803”. Electron microscopy, 13 ligands (CLA, BCR, SQD), 20 pockets (best druggability 0.86). MolNFT v1 #168525 on GenesisL1: 3D…
- PDB
- 6WJ6
- Type
- protein
- Length
- 1,898 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosystem II protein D1 2; Photosystem II CP47 reaction center protein; Photosystem II…
- EC
- 1.10.3.9
- UniProt
- P16033, P05429, P09193, P09192, P09190, P09191, P14835, Q54697, P15819, Q55354, P72701, P74787, P72575
- Ligands
- CLA, BCR, SQD, LHG, LMG, FME, PHO, PL9, DGD, BCT, HEM, FE2, CL
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 13 distinct chains · 58% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photosystem II protein D1 2 (EC 1.10.3.9) | protein | 302 | 62% helix, 3% strand | P16033 |
| B | Photosystem II CP47 reaction center protein | protein | 478 | 49% helix, 10% strand | P05429 |
| C | Photosystem II CP43 reaction center protein | protein | 415 | 58% helix, 5% strand | P09193 |
| D | Photosystem II D2 protein (EC 1.10.3.9) | protein | 342 | 62% helix, 3% strand | P09192 |
| E | Cytochrome B559 subunit alpha | protein | 72 | 54% helix, 0% strand | P09190 |
| F | Cytochrome B559 subunit beta | protein | 32 | 72% helix, 0% strand | P09191 |
| H | Photosystem II reaction center protein H | protein | 63 | 49% helix, 3% strand | P14835 |
| I | Photosystem II reaction center protein I | protein | 35 | 71% helix, 0% strand | Q54697 |
| K | Photosystem II reaction center protein K | protein | 35 | 71% helix, 0% strand | P15819 |
| L | Photosystem II reaction center protein L | protein | 31 | 74% helix, 3% strand | Q55354 |
| M | Photosystem II reaction center protein M | protein | 29 | 72% helix, 0% strand | P72701 |
| T | Photosystem II reaction center protein T | protein | 29 | 69% helix, 0% strand | P74787 |
| X | Photosystem II reaction center X protein | protein | 35 | 77% helix, 0% strand | P72575 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 35 copies · chains A, D, T, I, B, H, L, M, C, K, X
- BCR · Beta-carotene · ligand · 9 copies · chains A, I, B, M, C, K, D, F, H, X
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 7 copies · chains A, C, D, K, T, B, H, L, M, X
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 4 copies · chains B, D, L, M, A, T, C
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 3 copies · chains B, D, L, M, A, C, I, F
- FME · N-formylmethionine · ligand · 3 copies · chains A, I, D, M, T
- PHO · Pheophytin A · ligand · 2 copies · chains 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
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 2 copies · chains A, C, B, D, H
- BCT · Bicarbonate ion · ligand · chains A, D
- HEM · Protoporphyrin IX containing Fe · ligand · chains E, F
- FE2 · Fe (II) ion · metal · chains A, D
- CL · Chloride ion · ion · chains A, D
- LMT · Dodecyl-beta-D-maltoside · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.86 | 0.86 | 109 | DGD |
| 2 | 1119 | 0.85 | 0.85 | 96 | CLA, LHG |
| 3 | 1166 | 0.81 | 0.81 | 108 | CLA, DGD |
| 4 | 409 | 0.76 | 0.85 | 34 | FE2, PL9, BCT |
| 5 | 860 | 0.72 | 0.77 | 73 | CLA, LHG |
Interfaces
29 interfaces between chains.
- A–D · 4636 Ų buried · 43 hydrogen bonds · protein-protein
- B–D · 2611 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 1945 Ų buried · 9 hydrogen bonds · protein-protein
- B–H · 1903 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 1267 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6WJ6 · Cryo-EM structure of apo-Photosystem II from Synechocystis sp. PCC 6803 · 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 P16033
- Every structure of UniProt P05429
- Every structure of UniProt P09193
- Every structure of UniProt P09192
- Every structure of UniProt P09190
- Every structure of UniProt P09191
- Every structure of UniProt P14835
- Every structure of UniProt Q54697
- Every structure of UniProt P15819
- Every structure of UniProt Q55354
- Every structure of UniProt P72701
- Every structure of UniProt P74787
- Every structure of UniProt P72575
- Elsewhere: RCSB PDB 6WJ6 · PDBe 6WJ6 · UniProt P16033 · UniProt P05429 · UniProt P09193 · UniProt P09192 · UniProt P09190 · UniProt P09191 · UniProt P14835 · UniProt Q54697 · UniProt P15819 · UniProt Q55354 · UniProt P72701 · UniProt P74787 · UniProt P72575
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