Research workbench
Crystal structure of uncharacterized conserved protein pixa from burkholderia thailandensis
Analyse Crystal structure of uncharacterized conserved protein pixa from burkholderia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PIB
- Type
- protein
- Length
- 1,749 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inclusion body protein
- UniProt
- Q2SVW5
- Ligands
- CA, CL
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, H | Inclusion body protein | protein | 174 | 6% helix, 55% strand | Q2SVW5 |
| B, C, D, E, G, I | Inclusion body protein | protein | 176 | 7% helix, 56% strand | Q2SVW5 |
| J | Inclusion body protein | protein | 171 | 5% helix, 56% strand | Q2SVW5 |
Ligands and binding sites
- CA · Calcium ion · metal · 31 copies · chains A, B, C, D, F, E, G, H, J, I
- CL · Chloride ion · ion · 7 copies · chains A, C, B, D, F, E, G, H, J
- GOL · Glycerol · additive · 9 copies · chains A, B, C, D, G, H, I
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.75 | 0.98 | 22 | CA |
| 2 | 77 | 0.75 | 0.98 | 24 | CA |
| 3 | 75 | 0.75 | 0.98 | 22 | CA |
| 4 | 74 | 0.75 | 0.98 | 21 | CA |
| 5 | 68 | 0.74 | 0.99 | 22 | CA |
Interfaces
17 interfaces between chains.
- I–J · 2450 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 2368 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2356 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 2354 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 2350 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 4PIB · Crystal Structure of Uncharacterized Conserved Protein PixA from Burkholderia… · the same entry in another collection · chain H against H, 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 Q2SVW5
- Elsewhere: RCSB PDB 4PIB · PDBe 4PIB · UniProt Q2SVW5
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