MolNFT v1 · #186930 · protein + DNA
Updated crystal structure of replication initiator protein REPE54.
7RVA · DNA (5'- D(*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*…: “Updated crystal structure of replication initiator protein REPE54.”. X-ray diffraction, 2 ligands (MG, NA), 3 pockets (best druggability 0.57). MolNFT v1 #186930 on…
- PDB
- 7RVA
- Type
- protein + DNA
- Length
- 271 residues
- Chains
- 5
- 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, NA
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 29% 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 | 22 | — | — |
| C | Replication initiation protein | protein | 221 | 43% helix, 30% strand | P03856 |
| D | Unk-unk-unk | protein | 3 | 0% helix, 0% strand | — |
| E | Unk-unk-unk-unk | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
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 | 251 | 0.57 | 0.78 | 36 | NA |
| 2 | 52 | 0.42 | 0.83 | 17 | empty |
| 3 | 78 | 0.31 | 0.74 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–B · 994 Ų buried · 97 hydrogen bonds · nucleic-nucleic
- B–C · 894 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–C · 700 Ų buried · 18 hydrogen bonds · protein-nucleic
- C–D · 202 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 182 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7RVA · Updated Crystal Structure of Replication Initiator Protein REPE54. · the same entry in another collection · chain B against B, 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 0.98
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 7RVA · PDBe 7RVA · UniProt P03856
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