MolNFT v1 · #1655 · protein
Crystal structure of a phycourobilin-containing phycoerythrin
1B8D · Protein (rhodophytan phycoerythrin (alpha chain) ): “Crystal structure of a phycourobilin-containing phycoerythrin”. X-ray diffraction, 2 ligands (PEB, PUB), 16 pockets (best druggability 0.70). MolNFT v1 #1655 on GenesisL1: 3D…
- PDB
- 1B8D
- Type
- protein
- Length
- 685 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (rhodophytan phycoerythrin (alpha chain) ); Protein (rhodophytan phycoerythrin…
- UniProt
- O36005, O36004
- Ligands
- PEB, PUB
- Pockets
- 16 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, K | Protein (rhodophytan phycoerythrin (alpha chain) ) | protein | 164 | 77% helix, 0% strand | O36005 |
| B, L | Protein (rhodophytan phycoerythrin (beta chain)) | protein | 177 | 73% helix, 0% strand | O36004 |
| G | Protein (rhodophytan phycoerythrin (gamma chain) ) | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- PEB · Phycoerythrobilin · ligand · 8 copies · chains A, B, G, K, L
- PUB · Phycourobilin · ligand · 2 copies · chains B, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 319 | 0.70 | 0.84 | 47 | empty |
| 2 | 336 | 0.70 | 0.83 | 49 | empty |
| 3 | 170 | 0.63 | 0.84 | 31 | PEB |
| 4 | 157 | 0.63 | 0.85 | 31 | PEB |
| 5 | 111 | 0.56 | 0.84 | 22 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1607 Ų buried · 19 hydrogen bonds · protein-protein
- K–L · 1582 Ų buried · 20 hydrogen bonds · protein-protein
- A–K · 980 Ų buried · 18 hydrogen bonds · protein-protein
- A–L · 377 Ų buried · 11 hydrogen bonds · protein-protein
- B–K · 370 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 4 covalent, 2 modified (phycoerythrobilin attachment, covalent ligand, nonstandard).
Compared structures
- 1B8D · Crystal structure of a phycourobilin-containing phycoerythrin · the same entry in another collection · chain K against K, TM-score 1.00
- O36005 · AlphaFold monomer V2.0 prediction for R-phycoerythrin alpha chain (O36005) · a predicted model of the same protein · chain A against A, TM-score 0.99
- O36004 · AlphaFold monomer V2.0 prediction for R-phycoerythrin beta chain (O36004) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O36005
- Every structure of UniProt O36004
- Elsewhere: RCSB PDB 1B8D · PDBe 1B8D · UniProt O36005 · UniProt O36004
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