Research workbench
Crystal structure of E. COLI primosomol protein prib bound to ssdna
Analyse Crystal structure of E. COLI primosomol protein prib bound to ssdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CCZ
- Type
- protein + DNA
- Length
- 254 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Primosomal replication protein N; 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP *TP*TP*TP*TP*T)-3'
- UniProt
- P07013
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Primosomal replication protein N | protein | 121 | 12% helix, 52% strand | P07013 |
| B | Primosomal replication protein N | protein | 118 | 16% helix, 53% strand | P07013 |
| C | 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP *TP*TP*TP*TP*T)-3' | dna | 15 | — | — |
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 576 | 0.73 | 0.81 | 52 | empty |
| 2 | 291 | 0.63 | 0.80 | 36 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1503 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 696 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–C · 236 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2CCZ · Crystal structure of E. coli primosomol protein PriB bound to ssDNA · the same entry in another collection · chain A against A, TM-score 1.00
- P07013 · AlphaFold monomer V2.0 prediction for primosomal replication protein N (P07013) · a predicted model of the same protein · chain B against A, TM-score 0.81
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 P07013
- Elsewhere: RCSB PDB 2CCZ · PDBe 2CCZ · UniProt P07013
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