Research workbench
Crystal structure of photosystem II
Analyse Crystal structure of photosystem II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IZL
- Type
- protein
- Length
- 4,297 residues
- Chains
- 28
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosystem II: subunit psba; Photosystem II: subunit psbb; Photosystem II: subunit psbc…
- UniProt
- P51765, Q9F1K9, P56150
- Ligands
- CLA, PHO, HEM, PLA, BCR, MN, FE
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 22 distinct chains · 22% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, J | Photosystem II: subunit psba | protein | 299 | 26% helix, 0% strand | P51765 |
| B | Photosystem II: subunit psbb | protein | 427 | 26% helix, 0% strand | — |
| C | Photosystem II: subunit psbc | protein | 349 | 37% helix, 0% strand | — |
| D, N | Photosystem II: subunit psbd | protein | 277 | 29% helix, 0% strand | — |
| E | Photosystem II: subunit psbe | protein | 35 | 23% helix, 0% strand | — |
| F | Photosystem II: subunit psbf | protein | 30 | 37% helix, 0% strand | — |
| G, R | Photosystem II: subunit psbg | protein | 220 | 0% helix, 0% strand | — |
| H | Photosystem II: subunit psbh | protein | 33 | 42% helix, 0% strand | — |
| I | Photosystem II: subunit psbi | protein | 26 | 42% helix, 0% strand | — |
| K, W | Photosystem II: subunit psbk | protein | 27 | 0% helix, 0% strand | Q9F1K9 |
| O | Photosystem II: subunit psbo | protein | 205 | 0% helix, 0% strand | — |
| U | Photosystem II: subunit psbu | protein | 97 | 7% helix, 0% strand | — |
| V | Photosystem II: subunit psbv | protein | 129 | 22% helix, 0% strand | P56150 |
| X, T, 1 | Photosystem II: subunit psbx | protein | 25 | 0% helix, 0% strand | — |
| L | Photosystem II: subunit psbb | protein | 424 | 26% helix, 0% strand | — |
| M | Photosystem II: subunit psbc | protein | 347 | 32% helix, 0% strand | — |
| P | Photosystem II: subunit psbe | protein | 17 | 47% helix, 0% strand | — |
| Q | Photosystem II: subunit psbf | protein | 26 | 27% helix, 0% strand | — |
| S | Photosystem II: subunit psbh | protein | 32 | 31% helix, 0% strand | — |
| Y | Photosystem II: subunit psbo | protein | 192 | 0% helix, 0% strand | — |
| Z | Photosystem II: subunit psbu | protein | 92 | 8% helix, 0% strand | — |
| 0 | Photosystem II: subunit psbv | protein | 115 | 20% helix, 0% strand | P56150 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 72 copies · chains A, D, B, G, C, K, H, J, L, R, N, M, W
- PHO · Pheophytin A · ligand · 4 copies · chains A, D, J, N
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains E, X, V, P, 1, 0
- PLA · 2-[(3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl)-amino]-2-methyl-succinic acid · ligand · 2 copies · chains D, N
- BCR · Beta-carotene · ligand · 2 copies · chains C, D
- MN · Manganese (II) ion · metal · 8 copies · chains A, J
- FE · Fe (III) ion · metal · 2 copies · chains D, N
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 | 951 | 0.85 | 0.86 | 162 | MN |
| 2 | 771 | 0.83 | 0.87 | 122 | MN |
| 3 | 993 | 0.79 | 0.81 | 103 | empty |
| 4 | 827 | 0.77 | 0.81 | 116 | empty |
| 5 | 488 | 0.74 | 0.83 | 96 | empty |
Interfaces
74 interfaces between chains.
- J–N · 2043 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 2000 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1309 Ų buried · 9 hydrogen bonds · protein-protein
- J–M · 1275 Ų buried · 9 hydrogen bonds · protein-protein
- C–O · 697 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 covalent (covalent ligand).
Compared structures
- 1IZL · Crystal Structure of Photosystem II · the same entry in another collection · chain O against O, 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 P51765
- Every structure of UniProt Q9F1K9
- Every structure of UniProt P56150
- Elsewhere: RCSB PDB 1IZL · PDBe 1IZL · UniProt P51765 · UniProt Q9F1K9 · UniProt P56150
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