MolNFT v1 · #179561 · protein + RNA
Crystal structure of bacillus halodurans oapb in complex with its ole RNA target (crystal form I)
7K9D · Ole-associated protein B: “Crystal structure of bacillus halodurans oapb in complex with its ole RNA target (crystal form I)”. X-ray diffraction, 1 ligand (NCO), 2 pockets (best druggability 0.55). MolNFT v1 #179561 on GenesisL1: 3D…
- 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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