MolNFT v1 · #27285 · protein
High resolution crystal structure of phycoerythrin 545 from the marine cryptophyte rhodomonas CS24
1XF6 · Phycoerythrin alpha-3 chain: “High resolution crystal structure of phycoerythrin 545 from the marine cryptophyte rhodomonas CS24”. X-ray diffraction, 4 ligands (PEB, DBV, MG), 8 pockets (best druggability 0.85). MolNFT v1 #27285 on…
- 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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