Research workbench
Structure of the mutant D105N of phycoerythrobilin synthase pebs from the cyanophage P-SSM2 in complex with bound substrate biliverdin ixa
Analyse Structure of the mutant D105N of phycoerythrobilin synthase pebs from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X9I
- Type
- protein
- Length
- 828 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phycobilin synthase
- EC
- 1.3.7.6
- UniProt
- Q58MU6
- Ligands
- BLA, SO4
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Phycobilin synthase (EC 1.3.7.6) | protein | 209 | 33% helix, 30% strand | Q58MU6 |
| B, C | Phycobilin synthase (EC 1.3.7.6) | protein | 205 | 33% helix, 31% strand | Q58MU6 |
Ligands and binding sites
- BLA · Biliverdine IX alpha · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.74 | 0.87 | 36 | BLA |
| 2 | 307 | 0.72 | 0.84 | 42 | BLA |
| 3 | 249 | 0.68 | 0.84 | 36 | BLA |
| 4 | 252 | 0.66 | 0.83 | 34 | BLA |
| 5 | 254 | 0.51 | 0.75 | 47 | empty |
Interfaces
3 interfaces between chains.
- A–C · 616 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 282 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 46 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2X9I · Structure of the Mutant D105N of Phycoerythrobilin Synthase PebS from the Cyanophage… · 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 Q58MU6
- Elsewhere: RCSB PDB 2X9I · PDBe 2X9I · UniProt Q58MU6
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