Research workbench
Replication initiator dnaa bound to amppcp and single-stranded DNA
Analyse Replication initiator dnaa bound to amppcp and single-stranded DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R8F
- Type
- protein + DNA
- Length
- 1,288 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chromosomal replication initiator protein dnaa…
- UniProt
- O66659
- Ligands
- ACP, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Chromosomal replication initiator protein dnaa | protein | 319 | 60% helix, 8% strand | O66659 |
| E | 5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3' | dna | 12 | — | — |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1048 | 0.85 | 0.86 | 121 | MG, ACP |
| 2 | 697 | 0.80 | 0.84 | 73 | empty |
| 3 | 612 | 0.78 | 0.84 | 65 | empty |
| 4 | 627 | 0.78 | 0.84 | 71 | MG, ACP |
| 5 | 685 | 0.78 | 0.82 | 73 | MG, ACP |
Interfaces
7 interfaces between chains.
- B–C · 1897 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1897 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1833 Ų buried · 20 hydrogen bonds · protein-protein
- B–E · 289 Ų buried · 7 hydrogen bonds · protein-nucleic
- C–E · 284 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 3R8F · Replication initiator DnaA bound to AMPPCP and single-stranded DNA · the same entry in another collection · chain E against E, TM-score 1.00
- O66659 · AlphaFold monomer V2.0 prediction for chromosomal replication initiator protein dnaa… · a predicted model of the same protein · chain D against A, TM-score 0.86
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 O66659
- Elsewhere: RCSB PDB 3R8F · PDBe 3R8F · UniProt O66659
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