Research workbench
Structure of pyrr protein from bacillus subtilis with gmp
Analyse Structure of pyrr protein from bacillus subtilis with gmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P86
- Type
- protein
- Length
- 700 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional protein pyrr
- Ligands
- 5GP
- Pockets
- 10 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional protein pyrr | protein | 177 | 31% helix, 36% strand | — |
| B | Bifunctional protein pyrr | protein | 175 | 30% helix, 36% strand | — |
| C, D | Bifunctional protein pyrr | protein | 174 | 32% helix, 36% strand | — |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 422 | 0.67 | 0.80 | 49 | 5GP |
| 2 | 335 | 0.59 | 0.77 | 37 | 5GP |
| 3 | 235 | 0.58 | 0.79 | 39 | empty |
| 4 | 232 | 0.54 | 0.77 | 30 | 5GP |
| 5 | 251 | 0.53 | 0.76 | 29 | 5GP |
Interfaces
6 interfaces between chains.
- C–D · 1039 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 996 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 548 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 522 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 78 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4P86 · Structure of PyrR protein from Bacillus subtilis with GMP · 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
- Elsewhere: RCSB PDB 4P86 · PDBe 4P86
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