Research workbench
Crystal structure of the ccc complex of the N-terminal domain of pria
Analyse Crystal structure of the ccc complex of the N-terminal domain of pria in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D7H
- Type
- protein + DNA
- Length
- 407 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Primosomal protein N'; DNA (5'-D(P*CP*CP*C)-3')
- EC
- 3.6.4.-
- UniProt
- P17888
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 26% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Primosomal protein N' (EC 3.6.4.-) | protein | 102 | 28% helix, 26% strand | P17888 |
| B | Primosomal protein N' (EC 3.6.4.-) | protein | 97 | 26% helix, 21% strand | P17888 |
| C | Primosomal protein N' (EC 3.6.4.-) | protein | 105 | 24% helix, 26% strand | P17888 |
| D | Primosomal protein N' (EC 3.6.4.-) | protein | 102 | 25% helix, 27% strand | P17888 |
| E | DNA (5'-D(P*CP*CP*C)-3') | dna | 1 | — | — |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 724 | 0.73 | 0.79 | 42 | empty |
| 2 | 788 | 0.72 | 0.77 | 75 | empty |
| 3 | 104 | 0.55 | 0.84 | 26 | empty |
| 4 | 70 | 0.46 | 0.83 | 18 | empty |
| 5 | 58 | 0.36 | 0.79 | 16 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2175 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 1899 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 796 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 281 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 248 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 2D7H · Crystal structure of the ccc complex of the N-terminal domain of PriA · the same entry in another collection · chain D against D, TM-score 1.00
- P17888 · AlphaFold monomer V2.0 prediction for primosomal protein N' (P17888) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 P17888
- Elsewhere: RCSB PDB 2D7H · PDBe 2D7H · UniProt P17888
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