Research workbench
High resolution crystal structure of phycoerythrin 545 from the marine cryptophyte rhodomonas CS24
Analyse High resolution crystal structure of phycoerythrin 545 from the marine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XF6
- Type
- protein
- Length
- 493 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phycoerythrin alpha-3 chain; Phycoerythrin alpha-2 chain; B-phycoerythrin beta chain
- UniProt
- Q00433, P30943, P27198
- Ligands
- PEB, DBV, MG, CL
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phycoerythrin alpha-3 chain | protein | 76 | 20% helix, 24% strand | Q00433 |
| B | Phycoerythrin alpha-2 chain | protein | 67 | 27% helix, 27% strand | P30943 |
| C | B-phycoerythrin beta chain | protein | 173 | 70% helix, 2% strand | P27198 |
| D | B-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
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1190 | 0.85 | 0.86 | 132 | CL, PEB |
| 2 | 204 | 0.69 | 0.86 | 36 | PEB |
| 3 | 195 | 0.67 | 0.86 | 36 | PEB |
| 4 | 230 | 0.63 | 0.82 | 39 | DBV |
| 5 | 92 | 0.63 | 0.89 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2230 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 2018 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 679 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 643 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 157 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 3 modified, 2 covalent (phycoerythrobilin attachment, covalent ligand, nonstandard, hydroxylation).
Compared structures
- 1XF6 · High resolution crystal structure of phycoerythrin 545 from the marine cryptophyte… · 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
- P30943 · AlphaFold monomer V2.0 prediction for phycoerythrin alpha-2 chain, chloroplastic (P30943) · a predicted model of the same protein · chain B against A, TM-score 0.97
- 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 0.84
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 P30943
- Every structure of UniProt P27198
- Elsewhere: RCSB PDB 1XF6 · PDBe 1XF6 · UniProt Q00433 · UniProt P30943 · UniProt P27198
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