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Crystal structure of bacillus halodurans oapb in complex with its ole RNA target (crystal form I)
Analyse Crystal structure of bacillus halodurans oapb in complex with its ole RNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K9D
- Type
- protein + RNA
- Length
- 149 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ole-associated protein B; Ole* RNA
- UniProt
- Q9KGD7
- Ligands
- NCO
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ole-associated protein B | protein | 89 | 34% helix, 31% strand | Q9KGD7 |
| B | Ole* RNA | rna | 60 | — | — |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 6 copies · chains B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A, 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 | 394 | 0.55 | 0.74 | 27 | EPE, NCO |
| 2 | 299 | 0.48 | 0.73 | 18 | NCO |
Interfaces
1 interface between chains.
- A–B · 690 Ų buried · 28 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 7K9D · Crystal structure of Bacillus halodurans OapB in complex with its OLE RNA target (crystal… · 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 Q9KGD7
- Elsewhere: RCSB PDB 7K9D · PDBe 7K9D · UniProt Q9KGD7
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