Research workbench
Crystal structure of phycoerythrin 545 from the marine cryptophyte rhodomonas CS24
Analyse Crystal structure of phycoerythrin 545 from the marine cryptophyte rhodomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QGW
- Type
- protein
- Length
- 489 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (cryptophytan phycoerythrin (alpha-1 chain)); Protein (cryptophytan phycoerythrin…
- UniProt
- Q00433, P27198
- Ligands
- PEB, DBV, MG, CL
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (cryptophytan phycoerythrin (alpha-1 chain)) | protein | 76 | 20% helix, 24% strand | Q00433 |
| B | Protein (cryptophytan phycoerythrin (alpha-2 chain)) | protein | 67 | 27% helix, 27% strand | Q00433 |
| C | Protein (cryptophytan phycoerythrin (beta chain)) | protein | 169 | 72% helix, 2% strand | P27198 |
| D | Protein (cryptophytan phycoerythrin (beta chain)) | protein | 177 | 72% helix, 2% strand | P27198 |
Ligands and binding sites
- PEB · Phycoerythrobilin · ligand · 6 copies · chains A, C, B, D
- DBV · 15,16-dihydrobiliverdin · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, B, D
- CL · Chloride ion · ion · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.85 | 0.88 | 88 | CL, PEB |
| 2 | 196 | 0.67 | 0.86 | 36 | PEB |
| 3 | 191 | 0.67 | 0.86 | 34 | PEB |
| 4 | 285 | 0.67 | 0.83 | 45 | PEB |
| 5 | 402 | 0.66 | 0.79 | 54 | DBV |
Interfaces
6 interfaces between chains.
- A–C · 2191 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 2031 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 687 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 644 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 177 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 4 modified, 2 covalent (phycoerythrobilin attachment, covalent ligand, hydroxylation, nonstandard).
Compared structures
- 1QGW · Crystal structure of phycoerythrin 545 from the marine cryptophyte rhodomonas CS24 · the same entry in another collection · chain D against D, TM-score 1.00
- Q00433 · AlphaFold monomer V2.0 prediction for phycoerythrin alpha-3 chain, chloroplastic (Q00433) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P27198 · AlphaFold monomer V2.0 prediction for B-phycoerythrin beta chain (P27198) · a predicted model of the same protein · chain C against A, TM-score 0.86
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 Q00433
- Every structure of UniProt P27198
- Elsewhere: RCSB PDB 1QGW · PDBe 1QGW · UniProt Q00433 · UniProt P27198
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