Research workbench
Crystal structure of agrobacterium tumefaciens VIRE2 in complex with its chaperone VIRE1: a novel fold and implications for DNA binding
Analyse Crystal structure of agrobacterium tumefaciens VIRE2 in complex with its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BTP
- Type
- protein
- Length
- 414 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single-strand DNA-binding protein; Protein VIRE1
- UniProt
- P08062, P08063
- Ligands
- NH4
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Single-strand DNA-binding protein | protein | 386 | 33% helix, 21% strand | P08062 |
| B | Protein VIRE1 | protein | 28 | 50% helix, 0% strand | P08063 |
Ligands and binding sites
- NH4 · Ammonium ion · ion · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.64 | 0.79 | 58 | empty |
| 2 | 324 | 0.60 | 0.78 | 31 | PEG |
| 3 | 231 | 0.59 | 0.80 | 27 | empty |
| 4 | 182 | 0.50 | 0.77 | 27 | NH4 |
| 5 | 117 | 0.44 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1392 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3BTP · Crystal structure of Agrobacterium tumefaciens VirE2 in complex with its chaperone VirE1… · the same entry in another collection · chain A against A, TM-score 1.00
- P08062 · AlphaFold monomer V2.0 prediction for single-strand DNA-binding protein (P08062) · a predicted model of the same protein · chain A against A, TM-score 0.62
- P08063 · AlphaFold monomer V2.0 prediction for protein VIRE1 (P08063) · a predicted model of the same protein · chain B against A, TM-score 0.58
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 P08062
- Every structure of UniProt P08063
- Elsewhere: RCSB PDB 3BTP · PDBe 3BTP · UniProt P08062 · UniProt P08063
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