MolNFT v1 · #74294 · protein
X-ray structure of phycobilisome lcm core-membrane linker polypeptide (fragment 254-400) from synechocystis sp. pcc 6803, northeast structural genomics consortium target SGR209C
3OSJ: “X-ray structure of phycobilisome lcm core-membrane linker polypeptide (fragment 254-400) from synechocystis…”. X-ray diffraction, 2 ligands (NA, NO3), 6 pockets (best druggability 0.65). MolNFT v1 #74294 on GenesisL1: 3D structure…
- PDB
- 3OSJ
- Type
- protein
- Length
- 538 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phycobilisome lcm core-membrane linker polypeptide
- UniProt
- Q55544
- Ligands
- NA, NO3
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Phycobilisome lcm core-membrane linker polypeptide | protein | 135 | 68% helix, 1% strand | Q55544 |
| B | Phycobilisome lcm core-membrane linker polypeptide | protein | 136 | 64% helix, 1% strand | Q55544 |
| C | Phycobilisome lcm core-membrane linker polypeptide | protein | 132 | 67% helix, 2% strand | Q55544 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 611 | 0.65 | 0.76 | 56 | empty |
| 2 | 356 | 0.59 | 0.76 | 40 | empty |
| 3 | 146 | 0.48 | 0.78 | 23 | empty |
| 4 | 112 | 0.40 | 0.75 | 14 | empty |
| 5 | 111 | 0.38 | 0.74 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–D · 454 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 400 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 207 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 132 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3OSJ · X-Ray Structure of Phycobilisome LCM core-membrane linker polypeptide (fragment 254-400)… · the same entry in another collection · chain D against D, TM-score 1.00
- Q55544 · AlphaFold monomer V2.0 prediction for phycobiliprotein apce (Q55544) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q55544
- Elsewhere: RCSB PDB 3OSJ · PDBe 3OSJ · UniProt Q55544
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