MolNFT v1 · #187653 · protein + DNA
Replication initiator protein REPE54 and cognate DNA sequence with terminal three prime phosphates chemically crosslinked (5 MG/ML edc, 12 hours).
7SOZ · DNA (5'- D(*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*…: “Replication initiator protein REPE54 and cognate DNA sequence with terminal three prime phosphates chemically…”. X-ray diffraction, 1 ligand (MG), 3 pockets (best…
- PDB
- 7SOZ
- Type
- protein + DNA
- Length
- 266 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*A)- 3'); DNA…
- UniProt
- Q0E856
- Ligands
- MG
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 26% 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*A)- 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*A)- 3') | dna | 21 | — | — |
| C | Repb family plasmid replication initiator protein | protein | 224 | 40% helix, 26% strand | Q0E856 |
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 | 437 | 0.65 | 0.79 | 42 | MG |
| 2 | 91 | 0.45 | 0.80 | 16 | empty |
| 3 | 55 | 0.28 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 951 Ų buried · 73 hydrogen bonds · nucleic-nucleic
- B–C · 885 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–C · 681 Ų buried · 16 hydrogen bonds · protein-nucleic
Compared structures
- 7SOZ · Replication Initiator Protein REPE54 and cognate DNA sequence with terminal three prime… · 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 Q0E856
- Elsewhere: RCSB PDB 7SOZ · PDBe 7SOZ · UniProt Q0E856
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