Research workbench
Light harvesting complex PC612 from the cryptophyte hemiselmis virescens M1635
Analyse Light harvesting complex PC612 from the cryptophyte hemiselmis virescens M1635 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LM6
- Type
- protein
- Length
- 476 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cryptophyte phycocyanin alpha chain; Cryptophyte phycocyanin beta chain
- Ligands
- CYC, DBV
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 63% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cryptophyte phycocyanin alpha chain | protein | 62 | 16% helix, 29% strand | — |
| B | Cryptophyte phycocyanin beta chain | protein | 177 | 71% helix, 2% strand | — |
| D | Cryptophyte phycocyanin beta chain | protein | 175 | 73% helix, 2% strand | — |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 6 copies · chains A, B, C, D
- DBV · 15,16-dihydrobiliverdin · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.75 | 0.79 | 98 | empty |
| 2 | 515 | 0.72 | 0.81 | 53 | CYC |
| 3 | 204 | 0.63 | 0.83 | 35 | CYC |
| 4 | 187 | 0.63 | 0.83 | 35 | CYC |
| 5 | 156 | 0.56 | 0.82 | 21 | CYC |
Interfaces
5 interfaces between chains.
- A–B · 1899 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1859 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 341 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 329 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 119 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor, 4 covalent (phycocyanobilin attachment, covalent ligand).
Compared structures
- 4LM6 · Light harvesting complex PC612 from the cryptophyte Hemiselmis virescens M1635 · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 4LM6 · PDBe 4LM6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.