Research workbench
Crystal structure of putative plasmid partition protein (BB_S35) from borrelia burgdorferi B31 bound to amppnp
Analyse Crystal structure of putative plasmid partition protein (BB_S35) from borrelia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TVK
- Type
- protein
- Length
- 479 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pf-32 protein
- UniProt
- H7C7Q1
- Ligands
- ANP, LI
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pf-32 protein | protein | 237 | 41% helix, 18% strand | H7C7Q1 |
| B | Pf-32 protein | protein | 242 | 44% helix, 19% strand | H7C7Q1 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- LI · Lithium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.79 | 0.81 | 115 | ANP |
| 2 | 222 | 0.65 | 0.83 | 34 | empty |
| 3 | 65 | 0.51 | 0.85 | 20 | empty |
| 4 | 65 | 0.32 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1027 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5TVK · Crystal Structure of putative plasmid partition protein (BB_S35) from Borrelia… · 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 H7C7Q1
- Elsewhere: RCSB PDB 5TVK · PDBe 5TVK · UniProt H7C7Q1
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