Research workbench
Crystal structure of a DUF2131 family protein (SAMA_2911) from shewanella amazonensis SB2B at 2.50 a resolution
Analyse Crystal structure of a DUF2131 family protein (SAMA_2911) from shewanella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KE2
- Type
- protein
- Length
- 296 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein YP_928783.1
- UniProt
- A1S9Q7
- Ligands
- NO3
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein YP_928783.1 | protein | 103 | 56% helix, 12% strand | A1S9Q7 |
| B | Uncharacterized protein YP_928783.1 | protein | 96 | 56% helix, 13% strand | A1S9Q7 |
| C | Uncharacterized protein YP_928783.1 | protein | 97 | 56% helix, 12% strand | A1S9Q7 |
Ligands and binding sites
- NO3 · Nitrate ion · ion · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.60 | 0.74 | 53 | EDO |
| 2 | 123 | 0.41 | 0.76 | 20 | empty |
| 3 | 50 | 0.28 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 549 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 195 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 92 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 3KE2 · CRYSTAL STRUCTURE OF a DUF2131 family protein (SAMA_2911) FROM SHEWANELLA AMAZONENSIS… · 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 A1S9Q7
- Elsewhere: RCSB PDB 3KE2 · PDBe 3KE2 · UniProt A1S9Q7
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