MolNFT v1 · #51845 · protein
The structure of phycoerythrin from gloeobacter violaceus
2VJH · Phycoerythrin alpha chain: “The structure of phycoerythrin from gloeobacter violaceus”. X-ray diffraction, 2 ligands (PEB, PUB), 13 pockets (best druggability 0.70). MolNFT v1 #51845 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2VJH
- Type
- protein
- Length
- 682 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phycoerythrin alpha chain; Phycoerythrin beta subunit
- UniProt
- Q7NLD7, Q7NLD6
- Ligands
- PEB, PUB
- Pockets
- 13 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Phycoerythrin alpha chain | protein | 164 | 77% helix, 0% strand | Q7NLD7 |
| B, D | Phycoerythrin beta subunit | protein | 177 | 74% helix, 0% strand | Q7NLD6 |
Ligands and binding sites
- PEB · Phycoerythrobilin · ligand · 8 copies · chains A, B, C, D
- PUB · Phycourobilin · ligand · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 416 | 0.70 | 0.82 | 57 | PEB |
| 2 | 313 | 0.68 | 0.83 | 40 | empty |
| 3 | 127 | 0.68 | 0.89 | 28 | PEB |
| 4 | 113 | 0.67 | 0.90 | 28 | PEB |
| 5 | 130 | 0.56 | 0.82 | 29 | PEB |
Interfaces
5 interfaces between chains.
- C–D · 1581 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1578 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 928 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 393 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 388 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 4 covalent, 2 modified (phycoerythrobilin attachment, covalent ligand, nonstandard).
Compared structures
- 2VJH · The structure of Phycoerythrin from Gloeobacter violaceus · 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
- Every structure of UniProt Q7NLD7
- Every structure of UniProt Q7NLD6
- Elsewhere: RCSB PDB 2VJH · PDBe 2VJH · UniProt Q7NLD7 · UniProt Q7NLD6
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