MolNFT v1 · #51427 · protein
Crystal structure of the N-terminal domain of dnad from bacillus subtilis
2V79 · DNA replication protein dnad: “Crystal structure of the N-terminal domain of dnad from bacillus subtilis”. X-ray diffraction, 2 ligands (NA, CL), 1 pocket (best druggability 0.31). MolNFT v1 #51427 on GenesisL1: 3D structure…
- PDB
- 2V79
- Type
- protein
- Length
- 232 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA replication protein dnad
- UniProt
- P39787
- Ligands
- NA, CL
- Pockets
- 1 · best druggability 0.31
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA replication protein dnad | protein | 115 | 59% helix, 15% strand | P39787 |
| B | DNA replication protein dnad | protein | 117 | 59% helix, 15% strand | P39787 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.31 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1576 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 2V79 · Crystal Structure of the N-terminal domain of DnaD from Bacillus Subtilis · the same entry in another collection · chain A against A, TM-score 1.00
- P39787 · AlphaFold monomer V2.0 prediction for DNA replication protein dnad (P39787) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P39787
- Elsewhere: RCSB PDB 2V79 · PDBe 2V79 · UniProt P39787
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