MolNFT v2 · #221050 · protein + DNA
Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence with 1 sticky bases and 3' terminal phosphates and crosslinked with EDC.
8TIY · DNA(5'-D(CP*CP*CP*GP*GP*AP*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*…: “Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded…”. X-ray diffraction at 3.11, 1 ligand (MG), 5 pockets (best…
- PDB
- 8TIY
- Type
- protein + DNA
- Length
- 272 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.11
- Source
- Escherichia coli K-12; SYNTHETIC CONSTRUCT
- Molecule
- DNA(5'-D(CP*CP*CP*GP*GP*AP*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*AP*GP*…
- UniProt
- P03856
- Ligands
- MG
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · resolution 3.11 · 3 distinct chains · 43% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA(5'-D(CP*CP*CP*GP*GP*AP*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*AP*GP*AP*CP*GP*GP*A)-')| | dna | 31 | — | — |
| B | DNA (5'-D(GP*CP*CP*GP*TP*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*GP*GP*TP*CP*CP*GP*GP*A)-3') | dna | 31 | — | — |
| C | Replication initiation protein | protein | 210 | 43% helix, 30% strand | P03856 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.61 | 0.77 | 50 | empty |
| 2 | 55 | 0.33 | 0.77 | 14 | empty |
| 3 | 70 | 0.31 | 0.75 | 18 | empty |
| 4 | 63 | 0.27 | 0.74 | 9 | empty |
| 5 | 52 | 0.27 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1358 Ų buried · 112 hydrogen bonds · nucleic-nucleic
- B–C · 929 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–C · 717 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
- P03856 · AlphaFold monomer V2.0 prediction for replication initiation protein (P03856) · a predicted model of the same protein · chain C 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 P03856
- Elsewhere: RCSB PDB 8TIY · PDBe 8TIY · UniProt P03856
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