Research workbench
Structure of the wt-phycoerythrobilin synthase pebs from the cyanophage P-SSM2 in complex with the bound substrate biliverdin ixa
Analyse Structure of the wt-phycoerythrobilin synthase pebs from the cyanophage P-SSM2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VGR
- Type
- protein
- Length
- 847 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 0.80
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyanobacterial phycoerythrobilin (EC 1.3.7.6) | protein | 210 | 32% helix, 30% strand | Q58MU6 |
| B | Cyanobacterial phycoerythrobilin (EC 1.3.7.6) | protein | 211 | 31% helix, 30% strand | Q58MU6 |
| C | Cyanobacterial phycoerythrobilin (EC 1.3.7.6) | protein | 213 | 31% helix, 34% strand | Q58MU6 |
| D | Cyanobacterial phycoerythrobilin (EC 1.3.7.6) | protein | 213 | 31% helix, 32% 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 | 543 | 0.80 | 0.86 | 71 | BLA |
| 2 | 538 | 0.75 | 0.83 | 68 | BLA |
| 3 | 342 | 0.71 | 0.83 | 37 | BLA |
| 4 | 483 | 0.67 | 0.79 | 71 | empty |
| 5 | 238 | 0.55 | 0.78 | 35 | empty |
Interfaces
6 interfaces between chains.
- A–D · 639 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 634 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 468 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 344 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 344 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2VGR · Structure of the WT-Phycoerythrobilin Synthase PebS from the Cyanophage P-SSM2 in Complex… · 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 2VGR · PDBe 2VGR · UniProt Q58MU6
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