Research workbench
X-ray structure of the putative se binding protein from pseudomonas fluorescens. northeast structural genomics consortium target PLR6.
Analyse X-ray structure of the putative se binding protein from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OBK
- Type
- protein
- Length
- 668 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SELT/SELW/SELH selenoprotein domain
- UniProt
- Q4KGC5
- Pockets
- 8 · best druggability 0.56
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G | SELT/SELW/SELH selenoprotein domain | protein | 84 | 36% helix, 29% strand | Q4KGC5 |
| B | SELT/SELW/SELH selenoprotein domain | protein | 85 | 31% helix, 28% strand | Q4KGC5 |
| C | SELT/SELW/SELH selenoprotein domain | protein | 82 | 30% helix, 29% strand | Q4KGC5 |
| E | SELT/SELW/SELH selenoprotein domain | protein | 80 | 38% helix, 30% strand | Q4KGC5 |
| F | SELT/SELW/SELH selenoprotein domain | protein | 86 | 35% helix, 28% strand | Q4KGC5 |
| H | SELT/SELW/SELH selenoprotein domain | protein | 83 | 37% helix, 29% strand | Q4KGC5 |
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.56 | 0.80 | 27 | empty |
| 2 | 186 | 0.52 | 0.78 | 25 | empty |
| 3 | 164 | 0.52 | 0.79 | 25 | empty |
| 4 | 158 | 0.52 | 0.79 | 27 | empty |
| 5 | 96 | 0.51 | 0.82 | 20 | empty |
Interfaces
12 interfaces between chains.
- E–F · 795 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 755 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 746 Ų buried · 5 hydrogen bonds · protein-protein
- G–H · 746 Ų buried · 7 hydrogen bonds · protein-protein
- F–G · 473 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2OBK · X-Ray structure of the putative Se binding protein from Pseudomonas fluorescens.… · 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 Q4KGC5
- Elsewhere: RCSB PDB 2OBK · PDBe 2OBK · UniProt Q4KGC5
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