Research workbench
Vbht fic protein from bartonella schoenbuchensis in complex with vbha antitoxin mutant E24G and ATP
Analyse Vbht fic protein from bartonella schoenbuchensis in complex with vbha antitoxin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZCB
- Type
- protein
- Length
- 247 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosine monophosphate-protein transferase vbht; Antitoxin vbha
- EC
- 2.7.7.-
- UniProt
- E6Z0R3, E6Z0R4
- Ligands
- ATP, MG
- Pockets
- 1 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosine monophosphate-protein transferase vbht (EC 2.7.7.-) | protein | 185 | 58% helix, 5% strand | E6Z0R3 |
| B | Antitoxin vbha | protein | 62 | 69% helix, 0% strand | E6Z0R4 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A, B
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 273 | 0.59 | 0.78 | 35 | ATP, MG, GOL |
Interfaces
1 interface between chains.
- A–B · 1607 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3ZCB · VbhT Fic protein from Bartonella schoenbuchensis in complex with VbhA antitoxin mutant… · the same entry in another collection · chain A against A, TM-score 1.00
- E6Z0R3 · AlphaFold monomer V2.0 prediction for protein adenylyltransferase vbht (E6Z0R3) · a predicted model of the same protein · chain A against A, TM-score 1.00
- E6Z0R4 · AlphaFold monomer V2.0 prediction for antitoxin vbha (E6Z0R4) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 E6Z0R3
- Every structure of UniProt E6Z0R4
- Elsewhere: RCSB PDB 3ZCB · PDBe 3ZCB · UniProt E6Z0R3 · UniProt E6Z0R4
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