Research workbench
Light harvesting complex PC645 from the cryptophyte chroomonas sp. CCMP270
Analyse Light harvesting complex PC645 from the cryptophyte chroomonas sp. CCMP270 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LMS
- Type
- protein
- Length
- 473 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cryptophyte phycocyanin (alpha-1 chain); Cryptophyte phycocyanin (beta chain)…
- Ligands
- CYC, M1V, DBV
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cryptophyte phycocyanin (alpha-1 chain) | protein | 80 | 19% helix, 23% strand | — |
| B | Cryptophyte phycocyanin (beta chain) | protein | 162 | 72% helix, 2% strand | — |
| C | Cryptophyte phycocyanin (alpha-2 chain) | protein | 68 | 24% helix, 26% strand | — |
| D | Cryptophyte phycocyanin (beta chain) | protein | 163 | 74% helix, 2% strand | — |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 4 copies · chains A, B, C, D
- M1V · mesobiliverdin IX(alpha) · ligand · 2 copies · chains A, B, C, D
- DBV · 15,16-dihydrobiliverdin · ligand · 2 copies · chains A, B, D, C
- P6G · Hexaethylene glycol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 632 | 0.82 | 0.87 | 85 | DBV |
| 2 | 443 | 0.70 | 0.81 | 59 | M1V |
| 3 | 175 | 0.69 | 0.88 | 32 | CYC |
| 4 | 226 | 0.67 | 0.85 | 34 | CYC |
| 5 | 438 | 0.67 | 0.79 | 55 | M1V |
Interfaces
6 interfaces between chains.
- A–B · 2314 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1977 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 751 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 689 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 343 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 4 cofactor, 2 modified (covalent ligand, phycocyanobilin attachment, nonstandard).
Compared structures
- 4LMS · Light harvesting complex PC645 from the cryptophyte Chroomonas sp. CCMP270 · 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 4LMS · PDBe 4LMS
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