Research workbench
Cryo-EM structure of adnab-amppnp-DNA complex
Analyse Cryo-EM structure of adnab-amppnp-DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PPU
- Type
- protein + DNA
- Length
- 1,382 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UVRD/REP helicase; ATP-dependent DNA helicase (UVRD/REP); DNA (29-mer)
- EC
- 3.6.4.12
- UniProt
- I7FZ56, A0A0D6HKQ2
- Ligands
- SF4, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 38% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | UVRD/REP helicase | protein | 752 | 36% helix, 7% strand | I7FZ56 |
| A | ATP-dependent DNA helicase (UVRD/REP) (EC 3.6.4.12) | protein | 601 | 41% helix, 11% strand | A0A0D6HKQ2 |
| X | DNA (29-mer) | dna | 29 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1048 | 0.84 | 0.85 | 103 | empty |
| 2 | 586 | 0.76 | 0.83 | 55 | SF4 |
| 3 | 634 | 0.67 | 0.76 | 68 | empty |
| 4 | 495 | 0.67 | 0.78 | 53 | empty |
| 5 | 296 | 0.62 | 0.79 | 36 | empty |
Interfaces
3 interfaces between chains.
- B–A · 5104 Ų buried · 35 hydrogen bonds · protein-protein
- B–X · 1302 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–X · 573 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 6PPU · Cryo-EM structure of AdnAB-AMPPNP-DNA complex · the same entry in another collection · chain B against B, 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 I7FZ56
- Every structure of UniProt A0A0D6HKQ2
- Elsewhere: RCSB PDB 6PPU · PDBe 6PPU · UniProt I7FZ56 · UniProt A0A0D6HKQ2
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