Research workbench
Structure of phycoerythrobilin synthase pebs from the cyanophage P- SSM2 in complex with the bound substrate biliverdin ixa
Analyse Structure of phycoerythrobilin synthase pebs from the cyanophage P- SSM2 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VCK
- Type
- protein
- Length
- 835 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyanobacterial phycoerythrobilin
- EC
- 1.3.7.6
- UniProt
- Q58MU6
- Ligands
- BLA
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyanobacterial phycoerythrobilin (EC 1.3.7.6) | protein | 208 | 33% helix, 32% strand | Q58MU6 |
| B, C, D | Cyanobacterial phycoerythrobilin (EC 1.3.7.6) | protein | 209 | 33% helix, 30% strand | Q58MU6 |
Ligands and binding sites
- BLA · Biliverdine IX alpha · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1173 | 0.81 | 0.82 | 133 | BLA |
| 2 | 247 | 0.74 | 0.87 | 35 | BLA |
| 3 | 282 | 0.73 | 0.86 | 37 | BLA |
| 4 | 258 | 0.70 | 0.84 | 36 | BLA |
| 5 | 253 | 0.55 | 0.77 | 32 | empty |
Interfaces
6 interfaces between chains.
- B–C · 621 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 604 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 535 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 354 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 324 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 2VCK · Structure of Phycoerythrobilin Synthase PebS from the Cyanophage P-SSM2 in Complex with… · 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 2VCK · PDBe 2VCK · UniProt Q58MU6
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