MolNFT v1 · #20433 · protein + DNA
Crystal structure of replication initiator protein REPE54 of mini-F plasmid complexed with an iteron DNA
1REP · DNA (5'- D(*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*…: “Crystal structure of replication initiator protein REPE54 of mini-F plasmid complexed with an iteron DNA”. X-ray diffraction, 1 ligand (MG), 3 pockets (best…
- PDB
- 1REP
- Type
- protein + DNA
- Length
- 256 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*AP*GP*T)- 3'); DNA…
- UniProt
- P03856
- Ligands
- MG
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'- D(*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*AP*GP*T)- 3') | dna | 21 | — | — |
| B | DNA (5'- D(*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*GP*GP*T)- 3') | dna | 21 | — | — |
| C | Protein (replication initiation protein) | protein | 214 | 43% helix, 27% strand | P03856 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 313 | 0.60 | 0.78 | 33 | MG |
| 2 | 82 | 0.33 | 0.75 | 25 | empty |
| 3 | 60 | 0.30 | 0.75 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 950 Ų buried · 71 hydrogen bonds · nucleic-nucleic
- B–C · 884 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–C · 654 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 1REP · Crystal structure of replication initiator protein REPE54 of mini-F plasmid complexed… · the same entry in another collection · chain A against A, TM-score 1.00
- 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 1REP · PDBe 1REP · UniProt P03856
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