Research workbench
Crystal structure of a putative endoribonuclease (SO_1960) from shewanella oneidensis mr-1 at 1.85 a resolution
Analyse Crystal structure of a putative endoribonuclease (SO_1960) from shewanella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OTM
- Type
- protein
- Length
- 456 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein
- UniProt
- Q8EFL1
- Ligands
- NA, CA
- Pockets
- 2 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein | protein | 152 | 37% helix, 27% strand | Q8EFL1 |
| B | Hypothetical protein | protein | 153 | 37% helix, 27% strand | Q8EFL1 |
| C | Hypothetical protein | protein | 151 | 37% helix, 27% strand | Q8EFL1 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B, C
- CA · Calcium ion · metal · chains A, B, C
- ACT · Acetate ion · additive · 6 copies · chains A, C, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.82 | 0.99 | 26 | CA |
| 2 | 53 | 0.24 | 0.72 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1057 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1051 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1039 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 2OTM · Crystal structure of a putative endoribonuclease (so_1960) from shewanella oneidensis… · 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 Q8EFL1
- Elsewhere: RCSB PDB 2OTM · PDBe 2OTM · UniProt Q8EFL1
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