Research workbench
Crystal structure of the N-terminal domain of dnad protein from geobacillus kaustophilus HTA426
Analyse Crystal structure of the N-terminal domain of dnad protein from geobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VN2
- Type
- protein
- Length
- 435 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chromosome replication initiation protein
- UniProt
- Q5KXY1
- Ligands
- MG
- Pockets
- 5 · best druggability 0.37
Structure
x-ray diffraction · 3 distinct chains · 59% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chromosome replication initiation protein | protein | 110 | 57% helix, 8% strand | Q5KXY1 |
| B | Chromosome replication initiation protein | protein | 109 | 58% helix, 8% strand | Q5KXY1 |
| C, D | Chromosome replication initiation protein | protein | 108 | 62% helix, 8% strand | Q5KXY1 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.37 | 0.75 | 21 | empty |
| 2 | 77 | 0.34 | 0.76 | 19 | empty |
| 3 | 60 | 0.30 | 0.75 | 17 | empty |
| 4 | 66 | 0.30 | 0.74 | 15 | empty |
| 5 | 68 | 0.29 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1742 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1693 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 202 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2VN2 · Crystal structure of the N-terminal domain of DnaD protein from Geobacillus kaustophilus… · 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 Q5KXY1
- Elsewhere: RCSB PDB 2VN2 · PDBe 2VN2 · UniProt Q5KXY1
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